Menu
GeneBe

3-112202262-T-C

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_183061.3(SLC9C1):c.2310A>G(p.Lys770=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00442 in 1,610,582 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0039 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0045 ( 41 hom. )

Consequence

SLC9C1
NM_183061.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.120
Variant links:
Genes affected
SLC9C1 (HGNC:31401): (solute carrier family 9 member C1) Predicted to enable potassium:proton antiporter activity and sodium:proton antiporter activity. Predicted to be involved in potassium ion transmembrane transport; regulation of intracellular pH; and sodium ion import across plasma membrane. Predicted to act upstream of or within flagellated sperm motility. Predicted to be located in motile cilium. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-112202262-T-C is Benign according to our data. Variant chr3-112202262-T-C is described in ClinVar as [Benign]. Clinvar id is 787585.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.12 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00448 (6532/1458468) while in subpopulation MID AF= 0.0297 (168/5664). AF 95% confidence interval is 0.026. There are 41 homozygotes in gnomad4_exome. There are 3318 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC9C1NM_183061.3 linkuse as main transcriptc.2310A>G p.Lys770= synonymous_variant 18/29 ENST00000305815.10
LOC124909407XR_007096003.1 linkuse as main transcriptn.6662T>C non_coding_transcript_exon_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC9C1ENST00000305815.10 linkuse as main transcriptc.2310A>G p.Lys770= synonymous_variant 18/292 NM_183061.3 P1Q4G0N8-1
SLC9C1ENST00000487372.5 linkuse as main transcriptc.2166A>G p.Lys722= synonymous_variant 17/281 Q4G0N8-2
SLC9C1ENST00000471295.1 linkuse as main transcriptc.*639A>G 3_prime_UTR_variant, NMD_transcript_variant 11/225

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00391
AC:
594
AN:
151996
Hom.:
3
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00101
Gnomad AMI
AF:
0.00768
Gnomad AMR
AF:
0.00605
Gnomad ASJ
AF:
0.0323
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00352
Gnomad FIN
AF:
0.000565
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.00427
Gnomad OTH
AF:
0.0115
GnomAD3 exomes
AF:
0.00568
AC:
1419
AN:
250030
Hom.:
15
AF XY:
0.00580
AC XY:
783
AN XY:
135104
show subpopulations
Gnomad AFR exome
AF:
0.000617
Gnomad AMR exome
AF:
0.00817
Gnomad ASJ exome
AF:
0.0377
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00334
Gnomad FIN exome
AF:
0.000509
Gnomad NFE exome
AF:
0.00504
Gnomad OTH exome
AF:
0.0112
GnomAD4 exome
AF:
0.00448
AC:
6532
AN:
1458468
Hom.:
41
Cov.:
30
AF XY:
0.00457
AC XY:
3318
AN XY:
725272
show subpopulations
Gnomad4 AFR exome
AF:
0.00120
Gnomad4 AMR exome
AF:
0.00883
Gnomad4 ASJ exome
AF:
0.0359
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00321
Gnomad4 FIN exome
AF:
0.000412
Gnomad4 NFE exome
AF:
0.00388
Gnomad4 OTH exome
AF:
0.00649
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00390
AC:
594
AN:
152114
Hom.:
3
Cov.:
32
AF XY:
0.00376
AC XY:
280
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.00101
Gnomad4 AMR
AF:
0.00604
Gnomad4 ASJ
AF:
0.0323
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00353
Gnomad4 FIN
AF:
0.000565
Gnomad4 NFE
AF:
0.00427
Gnomad4 OTH
AF:
0.0114
Alfa
AF:
0.00647
Hom.:
2
Bravo
AF:
0.00479
Asia WGS
AF:
0.00173
AC:
6
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
Cadd
Benign
3.4
Dann
Benign
0.54

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs112343617; hg19: chr3-111921109; API