rs5961738

Variant names:

• chrX-5578052-G-A
• rs5961738

Your query was ambiguous. Multiple possible variants found:

• chrX-5578052-G-A
• chrX-5578052-G-T

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 0.0151 in 110,622 control chromosomes in the GnomAD database, including 15 homozygotes. There are 495 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 0.015 (15 hom., 495 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0151 (1671/110622) while in subpopulation NFE AF = 0.0215 (1140/52937). AF 95% confidence interval is 0.0205. There are 15 homozygotes in GnomAd4. There are 495 alleles in the male GnomAd4 subpopulation. Median coverage is 23. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 15 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0151 AC: 1670 AN: 110575 Hom.: 15 Cov.: 23

Gnomad AFR AF: 0.00238

Gnomad AMI AF: 0.00294

Gnomad AMR AF: 0.0169

Gnomad ASJ AF: 0.0168

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00679

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.0298

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0195

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

GnomAD4 genome AF: 0.0151 AC: 1671 AN: 110622 Hom.: 15 Cov.: 23 AF XY: 0.0150 AC XY: 495 AN XY: 32908

African (AFR) AF: 0.00241 AC: 73 AN: 30299

American (AMR) AF: 0.0169 AC: 175 AN: 10347

Ashkenazi Jewish (ASJ) AF: 0.0168 AC: 44 AN: 2624

East Asian (EAS) AF: 0.00 AC: 0 AN: 3517

South Asian (SAS) AF: 0.00644 AC: 17 AN: 2641

European-Finnish (FIN) AF: 0.0313 AC: 183 AN: 5852

Middle Eastern (MID) AF: 0.0372 AC: 8 AN: 215

European-Non Finnish (NFE) AF: 0.0215 AC: 1140 AN: 52937

Other (OTH) AF: 0.0192 AC: 29 AN: 1509

Alfa AF: 0.000994 Hom.: 873

Bravo AF: 0.0150

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.91
DANN	Benign	0.90
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs5961738; hg19: chrX-5496093;