rs2721997

Variant names:

• chrX-51601840-C-A
• rs2721997

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0181 in 111,486 control chromosomes in the GnomAD database, including 20 homozygotes. There are 623 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 0.018 (20 hom., 623 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0181 (2013/111486) while in subpopulation NFE AF = 0.0276 (1467/53071). AF 95% confidence interval is 0.0265. There are 20 homozygotes in GnomAd4. There are 623 alleles in the male GnomAd4 subpopulation. Median coverage is 21. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 20 gene

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: 0.0181 AC: 2014 AN: 111437 Hom.: 20 Cov.: 21

Gnomad AFR AF: 0.00359

Gnomad AMI AF: 0.0552

Gnomad AMR AF: 0.0134

Gnomad ASJ AF: 0.00907

Gnomad EAS AF: 0.000282

Gnomad SAS AF: 0.0190

Gnomad FIN AF: 0.0228

Gnomad MID AF: 0.0672

Gnomad NFE AF: 0.0276

Gnomad OTH AF: 0.0213

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

GnomAD4 genome AF: 0.0181 AC: 2013 AN: 111486 Hom.: 20 Cov.: 21 AF XY: 0.0185 AC XY: 623 AN XY: 33710

African (AFR) AF: 0.00358 AC: 110 AN: 30744

American (AMR) AF: 0.0134 AC: 140 AN: 10469

Ashkenazi Jewish (ASJ) AF: 0.00907 AC: 24 AN: 2647

East Asian (EAS) AF: 0.000283 AC: 1 AN: 3536

South Asian (SAS) AF: 0.0187 AC: 49 AN: 2617

European-Finnish (FIN) AF: 0.0228 AC: 136 AN: 5976

Middle Eastern (MID) AF: 0.0737 AC: 16 AN: 217

European-Non Finnish (NFE) AF: 0.0276 AC: 1467 AN: 53071

Other (OTH) AF: 0.0210 AC: 32 AN: 1521

Alfa AF: 0.0263 Hom.: 533

Bravo AF: 0.0172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.50
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs2721997; hg19: chrX-51344692;