Variant chr1-27100305-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003047.5(SLC9A1):c.*2A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.966 in 1,518,694 control chromosomes in the GnomAD database, including 709,068 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.97 ( 71893 hom., cov: 34)

Exomes 𝑓: 0.97 ( 637175 hom. )

Consequence

SLC9A1
NM_003047.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -5.63

Variant links:

Genes affected

SLC9A1 (HGNC:11071): (solute carrier family 9 member A1) This gene encodes a Na+/H+ antiporter that is a member of the solute carrier family 9. The encoded protein is a plasma membrane transporter that is expressed in the kidney and intestine. This protein plays a central role in regulating pH homeostasis, cell migration and cell volume. This protein may also be involved in tumor growth. [provided by RefSeq, Sep 2011]

SLC9A1 links:

SLC9A1 (HGNC:):

SLC9A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 1-27100305-T-C is Benign according to our data. Variant chr1-27100305-T-C is described in ClinVar as [Benign]. Clinvar id is 1333120.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
SLC9A1	NM_003047.5 linkuse as main transcript	c.*2A>G	3_prime_UTR_variant	12/12	ENST00000263980.8	NP_003038.2	P19634-1B2RAH2
SLC9A1	XM_011542021.4 linkuse as main transcript	c.*2A>G	3_prime_UTR_variant	13/13		XP_011540323.1
SLC9A1	XM_047428769.1 linkuse as main transcript	c.*2A>G	3_prime_UTR_variant	16/16		XP_047284725.1
SLC9A1	NR_046474.2 linkuse as main transcript	n.2780A>G	non_coding_transcript_exon_variant	11/11

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLC9A1	ENST00000263980 linkuse as main transcript	c.*2A>G	3_prime_UTR_variant	12/12	1	NM_003047.5	ENSP00000263980.3	P19634-1
SLC9A1	ENST00000374089.5 linkuse as main transcript	n.1675A>G	non_coding_transcript_exon_variant	7/7	2
SLC9A1	ENST00000447808.1 linkuse as main transcript	n.*40A>G	downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.971

AC:

147825

AN:

152180

Hom.:

71834

Cov.:

show subpopulations

Gnomad AFR

AF:

0.989

Gnomad AMI

AF:

0.861

Gnomad AMR

AF:

0.976

Gnomad ASJ

AF:

0.911

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.989

Gnomad FIN

AF:

0.952

Gnomad MID

AF:

0.943

Gnomad NFE

AF:

0.964

Gnomad OTH

AF:

0.968

GnomAD3 exomes

AF:

0.969

AC:

171868

AN:

177446

Hom.:

83277

AF XY:

0.968

AC XY:

90728

AN XY:

93728

show subpopulations

Gnomad AFR exome

AF:

0.990

Gnomad AMR exome

AF:

0.980

Gnomad ASJ exome

AF:

0.895

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.990

Gnomad FIN exome

AF:

0.945

Gnomad NFE exome

AF:

0.961

Gnomad OTH exome

AF:

0.960

GnomAD4 exome

AF:

0.966

AC:

1319445

AN:

1366396

Hom.:

637175

Cov.:

AF XY:

0.966

AC XY:

646976

AN XY:

669862

show subpopulations

Gnomad4 AFR exome

AF:

0.987

Gnomad4 AMR exome

AF:

0.978

Gnomad4 ASJ exome

AF:

0.908

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.988

Gnomad4 FIN exome

AF:

0.946

Gnomad4 NFE exome

AF:

0.964

Gnomad4 OTH exome

AF:

0.964

GnomAD4 genome

AF:

0.971

AC:

147943

AN:

152298

Hom.:

71893

Cov.:

AF XY:

0.972

AC XY:

72424

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.989

Gnomad4 AMR

AF:

0.976

Gnomad4 ASJ

AF:

0.911

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.989

Gnomad4 FIN

AF:

0.952

Gnomad4 NFE

AF:

0.964

Gnomad4 OTH

AF:

0.969

Alfa

AF:

0.964

Hom.:

70526

Bravo

AF:

0.972

Asia WGS

AF:

0.993

AC:

3454

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Lichtenstein-Knorr syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.020

DANN

Benign

0.46

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over