rs2316350

Variant names:

• chrX-80094515-T-C
• rs2316350

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0919 in 111,689 control chromosomes in the GnomAD database, including 714 homozygotes. There are 3,042 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 0.092 (714 hom., 3042 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.614
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0918 AC: 10247 AN: 111634 Hom.: 716 Cov.: 22

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0167

Gnomad MID AF: 0.0297

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.0952

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0919 AC: 10264 AN: 111689 Hom.: 714 Cov.: 22 AF XY: 0.0897 AC XY: 3042 AN XY: 33923

African (AFR) AF: 0.182 AC: 5571 AN: 30677

American (AMR) AF: 0.168 AC: 1760 AN: 10491

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 70 AN: 2646

East Asian (EAS) AF: 0.397 AC: 1387 AN: 3495

South Asian (SAS) AF: 0.131 AC: 350 AN: 2671

European-Finnish (FIN) AF: 0.0167 AC: 102 AN: 6099

Middle Eastern (MID) AF: 0.0326 AC: 7 AN: 215

European-Non Finnish (NFE) AF: 0.0163 AC: 869 AN: 53182

Other (OTH) AF: 0.0966 AC: 148 AN: 1532

Alfa AF: 0.0584 Hom.: 425

Bravo AF: 0.112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.78
PhyloP100		0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2316350; hg19: chrX-79350014;