rs2721998

Variant names:

• chrX-51608675-A-C
• rs2721998

Your query was ambiguous. Multiple possible variants found:

• chrX-51608675-A-C
• chrX-51608675-A-G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.00485 in 111,562 control chromosomes in the GnomAD database, including 4 homozygotes. There are 153 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 0.0048 (4 hom., 153 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.575
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS2: High Homozygotes in GnomAd4 at 4 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.00487 AC: 543 AN: 111509 Hom.: 4 Cov.: 22

Gnomad AFR AF: 0.00104

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00382

Gnomad ASJ AF: 0.00303

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00534

Gnomad FIN AF: 0.00265

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00776

Gnomad OTH AF: 0.00602

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

GnomAD4 genome AF: 0.00485 AC: 541 AN: 111562 Hom.: 4 Cov.: 22 AF XY: 0.00453 AC XY: 153 AN XY: 33760

African (AFR) AF: 0.00104 AC: 32 AN: 30741

American (AMR) AF: 0.00382 AC: 40 AN: 10483

Ashkenazi Jewish (ASJ) AF: 0.00303 AC: 8 AN: 2641

East Asian (EAS) AF: 0.00 AC: 0 AN: 3523

South Asian (SAS) AF: 0.00498 AC: 13 AN: 2613

European-Finnish (FIN) AF: 0.00265 AC: 16 AN: 6039

Middle Eastern (MID) AF: 0.0507 AC: 11 AN: 217

European-Non Finnish (NFE) AF: 0.00776 AC: 412 AN: 53104

Other (OTH) AF: 0.00594 AC: 9 AN: 1515

Alfa AF: 0.00208 Hom.: 9

Bravo AF: 0.00488

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.41
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs2721998; hg19: chrX-51351527;