3-112155055-T-TA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_183061.3(SLC9C1):c.3365-7_3365-6insT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.68 (33450 hom., cov: 0)
  • Exomes 𝑓: 0.49 (16065 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC9C1 NM_183061.3 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.97

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-112155055-T-TA is Benign according to our data. Variant chr3-112155055-T-TA is described in ClinVar as [Benign]. Clinvar id is 769278.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC9C1	NM_183061.3	c.3365-7_3365-6insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000305815.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC9C1	ENST00000305815.10	c.3365-7_3365-6insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		2	NM_183061.3	P1
SLC9C1	ENST00000487372.5	c.3221-7_3221-6insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1
SLC9C1	ENST00000471295.1	c.*1694-7_*1694-6insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.679 AC: 98705 AN: 145264 Hom.: 33448 Cov.: 0

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.673

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.694

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.486 AC: 603620 AN: 1241774 Hom.: 16065 Cov.: 30 AF XY: 0.486 AC XY: 301364 AN XY: 619874

Gnomad4 AFR exome AF: 0.471

Gnomad4 AMR exome AF: 0.498

Gnomad4 ASJ exome AF: 0.474

Gnomad4 EAS exome AF: 0.504

Gnomad4 SAS exome AF: 0.483

Gnomad4 FIN exome AF: 0.467

Gnomad4 NFE exome AF: 0.487

Gnomad4 OTH exome AF: 0.488

GnomAD4 genome AF: 0.679 AC: 98724 AN: 145320 Hom.: 33450 Cov.: 0 AF XY: 0.680 AC XY: 47894 AN XY: 70412

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.695

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Aug 04, 2017

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs11369523; hg19: chr3-111873902;