rs5952606

Variant names:

• chrX-44648131-G-A
• rs5952606

Your query was ambiguous. Multiple possible variants found:

• chrX-44648131-G-A
• chrX-44648131-G-C
• chrX-44648131-G-T

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 0.163 in 110,875 control chromosomes in the GnomAD database, including 1,713 homozygotes. There are 5,584 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 0.16 (1713 hom., 5584 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

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: 0.163 AC: 18104 AN: 110822 Hom.: 1709 Cov.: 22

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0355

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.0723

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.163 AC: 18121 AN: 110875 Hom.: 1713 Cov.: 22 AF XY: 0.169 AC XY: 5584 AN XY: 33101

African (AFR) AF: 0.112 AC: 3422 AN: 30674

American (AMR) AF: 0.278 AC: 2878 AN: 10335

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 297 AN: 2627

East Asian (EAS) AF: 0.813 AC: 2779 AN: 3417

South Asian (SAS) AF: 0.194 AC: 506 AN: 2611

European-Finnish (FIN) AF: 0.219 AC: 1283 AN: 5868

Middle Eastern (MID) AF: 0.0605 AC: 13 AN: 215

European-Non Finnish (NFE) AF: 0.126 AC: 6648 AN: 52947

Other (OTH) AF: 0.180 AC: 271 AN: 1505

Alfa AF: 0.157 Hom.: 4953

Bravo AF: 0.178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.78
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs5952606; hg19: chrX-44507377;