3-112155055-TAAAA-TAAA

Variant names:

• chr3-112155055-TA-T
• rs11369523
• NM_183061.3:c.3365-7delT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_183061.3(SLC9C1):​c.3365-7delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00937 in 1,399,250 control chromosomes in the GnomAD database, including 3 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0035 (1 hom., cov: 0)
  • Exomes 𝑓: 0.010 (2 hom.)
• Consequence: SLC9C1 NM_183061.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9C1	NM_183061.3	c.3365-7delT		splice_region_variant, intron_variant	Intron 26 of 28	ENST00000305815.10	NP_898884.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC9C1	ENST00000305815.10	c.3365-7delT		splice_region_variant, intron_variant	Intron 26 of 28	2	NM_183061.3	ENSP00000306627.5
SLC9C1	ENST00000487372.5	c.3221-7delT		splice_region_variant, intron_variant	Intron 25 of 27	1		ENSP00000420688.1
SLC9C1	ENST00000471295.1	n.*1694-7delT		splice_region_variant, intron_variant	Intron 19 of 21	5		ENSP00000418371.1

Frequencies

GnomAD3 genomes AF: 0.00354 AC: 514 AN: 145364 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00134

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00124

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00108

Gnomad FIN AF: 0.00249

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00618

Gnomad OTH AF: 0.00305

GnomAD4 exome AF: 0.0100 AC: 12591 AN: 1253832 Hom.: 2 Cov.: 30 AF XY: 0.00983 AC XY: 6152 AN XY: 626088

Gnomad4 AFR exome AF: 0.00989

Gnomad4 AMR exome AF: 0.00549

Gnomad4 ASJ exome AF: 0.00830

Gnomad4 EAS exome AF: 0.000284

Gnomad4 SAS exome AF: 0.00466

Gnomad4 FIN exome AF: 0.00963

Gnomad4 NFE exome AF: 0.0111

Gnomad4 OTH exome AF: 0.00835

GnomAD4 genome AF: 0.00353 AC: 514 AN: 145418 Hom.: 1 Cov.: 0 AF XY: 0.00309 AC XY: 218 AN XY: 70470

Gnomad4 AFR AF: 0.00136

Gnomad4 AMR AF: 0.00124

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00109

Gnomad4 FIN AF: 0.00249

Gnomad4 NFE AF: 0.00617

Gnomad4 OTH AF: 0.00302

Alfa AF: 0.00219 Hom.: 903

ClinVar

Not reported in ClinVar

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;