rs2885913

Variant names:

• chrX-67895961-A-G
• rs2885913

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 0.472 in 109,332 control chromosomes in the GnomAD database, including 10,528 homozygotes. There are 14,181 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 0.47 (10528 hom., 14181 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 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: 0.471 AC: 51496 AN: 109288 Hom.: 10514 Cov.: 21

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.472 AC: 51556 AN: 109332 Hom.: 10528 Cov.: 21 AF XY: 0.448 AC XY: 14181 AN XY: 31640

African (AFR) AF: 0.783 AC: 23378 AN: 29865

American (AMR) AF: 0.393 AC: 4032 AN: 10253

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 834 AN: 2624

East Asian (EAS) AF: 0.313 AC: 1065 AN: 3398

South Asian (SAS) AF: 0.320 AC: 814 AN: 2542

European-Finnish (FIN) AF: 0.316 AC: 1803 AN: 5700

Middle Eastern (MID) AF: 0.461 AC: 95 AN: 206

European-Non Finnish (NFE) AF: 0.356 AC: 18715 AN: 52606

Other (OTH) AF: 0.475 AC: 700 AN: 1473

Alfa AF: 0.399 Hom.: 5102

Bravo AF: 0.492

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.42
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs2885913; hg19: chrX-67115803;