rs5912337

Variant names:

• chrX-79722599-A-G
• rs5912337

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 0.233 in 110,746 control chromosomes in the GnomAD database, including 2,363 homozygotes. There are 7,371 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 0.23 (2363 hom., 7371 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.359 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: 0.233 AC: 25752 AN: 110693 Hom.: 2360 Cov.: 22

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.151

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.233 AC: 25769 AN: 110746 Hom.: 2363 Cov.: 22 AF XY: 0.223 AC XY: 7371 AN XY: 32992

African (AFR) AF: 0.266 AC: 8103 AN: 30425

American (AMR) AF: 0.368 AC: 3828 AN: 10395

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 492 AN: 2630

East Asian (EAS) AF: 0.237 AC: 816 AN: 3447

South Asian (SAS) AF: 0.113 AC: 295 AN: 2614

European-Finnish (FIN) AF: 0.195 AC: 1159 AN: 5937

Middle Eastern (MID) AF: 0.161 AC: 35 AN: 218

European-Non Finnish (NFE) AF: 0.201 AC: 10631 AN: 52881

Other (OTH) AF: 0.225 AC: 341 AN: 1518

Alfa AF: 0.233 Hom.: 1662

Bravo AF: 0.254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.57
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs5912337; hg19: chrX-78978096;