rs3813932

Variant names:

• chrX-119086757-A-G
• rs3813932
• NM_001394962.1:c.3945T>C

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001394962.1(KIAA1210):​c.3945T>C​(p.Ser1315Ser) 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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
KIAA1210	NM_001394962.1	c.3945T>C	p.Ser1315Ser	synonymous_variant	Exon 9 of 12	ENST00000691062.1	NP_001381891.1
KIAA1210	NM_020721.1	c.4473T>C	p.Ser1491Ser	synonymous_variant	Exon 11 of 14		NP_065772.1
KIAA1210	XM_017029688.3	c.3990T>C	p.Ser1330Ser	synonymous_variant	Exon 9 of 12		XP_016885177.1
KIAA1210	XM_017029689.3	c.3792T>C	p.Ser1264Ser	synonymous_variant	Exon 8 of 11		XP_016885178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1210	ENST00000691062.1	c.3945T>C	p.Ser1315Ser	synonymous_variant	Exon 9 of 12		NM_001394962.1	ENSP00000510348.1
KIAA1210	ENST00000402510.2	c.4473T>C	p.Ser1491Ser	synonymous_variant	Exon 11 of 14	5		ENSP00000384670.2

Frequencies

GnomAD3 genomes AF: 0.154 AC: 16982 AN: 110623 Hom.: 1517 Cov.: 22

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

GnomAD2 exomes AF: 0.151 AC: 27035 AN: 178508 AF XY: 0.132

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 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

African (AFR) AF: 0.303 AC: 7990 AN: 26356

American (AMR) AF: 0.302 AC: 10517 AN: 34855

Ashkenazi Jewish (ASJ) AF: 0.0883 AC: 1707 AN: 19327

East Asian (EAS) AF: 0.467 AC: 14087 AN: 30177

South Asian (SAS) AF: 0.107 AC: 5738 AN: 53696

European-Finnish (FIN) AF: 0.0553 AC: 2239 AN: 40480

Middle Eastern (MID) AF: 0.120 AC: 496 AN: 4122

European-Non Finnish (NFE) AF: 0.0549 AC: 46172 AN: 841434

Other (OTH) AF: 0.110 AC: 5067 AN: 46023

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

African (AFR) AF: 0.292 AC: 8871 AN: 30365

American (AMR) AF: 0.229 AC: 2383 AN: 10427

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 234 AN: 2630

East Asian (EAS) AF: 0.463 AC: 1607 AN: 3471

South Asian (SAS) AF: 0.127 AC: 328 AN: 2580

European-Finnish (FIN) AF: 0.0475 AC: 281 AN: 5915

Middle Eastern (MID) AF: 0.107 AC: 23 AN: 215

European-Non Finnish (NFE) AF: 0.0559 AC: 2957 AN: 52896

Other (OTH) AF: 0.154 AC: 231 AN: 1499

Alfa AF: 0.0963 Hom.: 9471

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
PhyloP100		-0.93
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: rs3813932; hg19: chrX-118220720; COSMIC: COSV68175336;