3-112155055-TAAAA-TAAAAA

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_183061.3(SLC9C1):​c.3365-7dupT variant causes a splice region, 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, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.97
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_183061.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC9C1	NM_183061.3	MANE Select	c.3365-7dupT		splice_region intron	N/A	NP_898884.1	Q4G0N8-1
	SLC9C1	NM_001320531.2		c.3221-7dupT		splice_region intron	N/A	NP_001307460.1	Q4G0N8-2
	SLC9C1	NR_135297.2		n.2635-7dupT		splice_region intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC9C1	ENST00000305815.10	TSL:2 MANE Select	c.3365-7_3365-6insT		splice_region intron	N/A	ENSP00000306627.5	Q4G0N8-1
	SLC9C1	ENST00000487372.5	TSL:1	c.3221-7_3221-6insT		splice_region intron	N/A	ENSP00000420688.1	Q4G0N8-2
	SLC9C1	ENST00000471295.1	TSL:5	n.*1694-7_*1694-6insT		splice_region intron	N/A	ENSP00000418371.1	F8WCJ0

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

GnomAD2 exomes AF: 0.490 AC: 78633 AN: 160354 AF XY: 0.490

Gnomad AFR exome AF: 0.483

Gnomad AMR exome AF: 0.507

Gnomad ASJ exome AF: 0.483

Gnomad EAS exome AF: 0.505

Gnomad FIN exome AF: 0.482

Gnomad NFE exome AF: 0.488

Gnomad OTH exome AF: 0.488

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

African (AFR) AF: 0.471 AC: 12934 AN: 27462

American (AMR) AF: 0.498 AC: 16021 AN: 32180

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 10517 AN: 22198

East Asian (EAS) AF: 0.504 AC: 17803 AN: 35318

South Asian (SAS) AF: 0.483 AC: 34543 AN: 71588

European-Finnish (FIN) AF: 0.467 AC: 18269 AN: 39102

Middle Eastern (MID) AF: 0.506 AC: 2380 AN: 4700

European-Non Finnish (NFE) AF: 0.487 AC: 466013 AN: 957682

Other (OTH) AF: 0.488 AC: 25140 AN: 51544

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

African (AFR) AF: 0.604 AC: 23895 AN: 39564

American (AMR) AF: 0.768 AC: 11147 AN: 14516

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2122 AN: 3388

East Asian (EAS) AF: 0.901 AC: 4521 AN: 5018

South Asian (SAS) AF: 0.761 AC: 3492 AN: 4586

European-Finnish (FIN) AF: 0.617 AC: 5446 AN: 8826

Middle Eastern (MID) AF: 0.657 AC: 184 AN: 280

European-Non Finnish (NFE) AF: 0.694 AC: 46005 AN: 66272

Other (OTH) AF: 0.695 AC: 1378 AN: 1982

Alfa AF: 0.478 Hom.: 903

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-4.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11369523; hg19: chr3-111873902;