rs3813932

Positions:

• chrX-119086757-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001394962.1(KIAA1210):​c.3945T>C​(p.Ser1315=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.092 in 1,207,145 control chromosomes in the GnomAD database, including 7,346 homozygotes. There are 35,514 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.15 (1517 hom., 4921 hem., cov: 22)
  • Exomes 𝑓: 0.086 (5829 hom. 30593 hem.)
• Consequence: KIAA1210 NM_001394962.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

Genes affected

KIAA1210 (HGNC:29218): (KIAA1210) Predicted to be located in acrosomal vesicle. Predicted to colocalize with basal ectoplasmic specialization. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP7: Synonymous conserved (PhyloP=-0.932 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1210	NM_001394962.1	c.3945T>C	p.Ser1315=	synonymous_variant	9/12	ENST00000691062.1	NP_001381891.1
KIAA1210	NM_020721.1	c.4473T>C	p.Ser1491=	synonymous_variant	11/14		NP_065772.1
KIAA1210	XM_017029688.3	c.3990T>C	p.Ser1330=	synonymous_variant	9/12		XP_016885177.1
KIAA1210	XM_017029689.3	c.3792T>C	p.Ser1264=	synonymous_variant	8/11		XP_016885178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1210	ENST00000691062.1	c.3945T>C	p.Ser1315=	synonymous_variant	9/12		NM_001394962.1	ENSP00000510348	A2
KIAA1210	ENST00000402510.2	c.4473T>C	p.Ser1491=	synonymous_variant	11/14	5		ENSP00000384670	P2

Frequencies

GnomAD3 genomes AF: 0.154 AC: 16982 AN: 110623 Hom.: 1517 Cov.: 22 AF XY: 0.149 AC XY: 4901 AN XY: 32947

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.154

GnomAD3 exomes AF: 0.151 AC: 27035 AN: 178508 Hom.: 2692 AF XY: 0.132 AC XY: 8518 AN XY: 64722

Gnomad AFR exome AF: 0.301

Gnomad AMR exome AF: 0.316

Gnomad ASJ exome AF: 0.0935

Gnomad EAS exome AF: 0.460

Gnomad SAS exome AF: 0.111

Gnomad FIN exome AF: 0.0554

Gnomad NFE exome AF: 0.0572

Gnomad OTH exome AF: 0.122

GnomAD4 exome AF: 0.0857 AC: 94013 AN: 1096470 Hom.: 5829 Cov.: 33 AF XY: 0.0845 AC XY: 30593 AN XY: 361962

Gnomad4 AFR exome AF: 0.303

Gnomad4 AMR exome AF: 0.302

Gnomad4 ASJ exome AF: 0.0883

Gnomad4 EAS exome AF: 0.467

Gnomad4 SAS exome AF: 0.107

Gnomad4 FIN exome AF: 0.0553

Gnomad4 NFE exome AF: 0.0549

Gnomad4 OTH exome AF: 0.110

GnomAD4 genome AF: 0.154 AC: 17007 AN: 110675 Hom.: 1517 Cov.: 22 AF XY: 0.149 AC XY: 4921 AN XY: 33009

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.0890

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0475

Gnomad4 NFE AF: 0.0559

Gnomad4 OTH AF: 0.154

Alfa AF: 0.0759 Hom.: 5271

Bravo AF: 0.181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.23
DANN	Benign	0.61

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: rs3813932; hg19: chrX-118220720; COSMIC: COSV68175336;