3-112155055-TAAAA-TAAAAAAAAAAAAAAAAAAAAA

Variant names:

• chr3-112155055-T-TAAAAAAAAAAAAAAAAA
• rs11369523
• NM_183061.3:c.3365-7_3365-6insTTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_183061.3(SLC9C1):​c.3365-7_3365-6insTTTTTTTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• 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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9C1	NM_183061.3	c.3365-7_3365-6insTTTTTTTTTTTTTTTTT		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.3365-7_3365-6insTTTTTTTTTTTTTTTTT		splice_region_variant, intron_variant	Intron 26 of 28	2	NM_183061.3	ENSP00000306627.5
SLC9C1	ENST00000487372.5	c.3221-7_3221-6insTTTTTTTTTTTTTTTTT		splice_region_variant, intron_variant	Intron 25 of 27	1		ENSP00000420688.1
SLC9C1	ENST00000471295.1	n.*1694-7_*1694-6insTTTTTTTTTTTTTTTTT		splice_region_variant, intron_variant	Intron 19 of 21	5		ENSP00000418371.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;