rs1397631

Variant names:

• chrX-67132854-C-T
• rs1397631

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 0.0871 in 110,684 control chromosomes in the GnomAD database, including 410 homozygotes. There are 2,611 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 0.087 (410 hom., 2611 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 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: 0.0872 AC: 9643 AN: 110634 Hom.: 411 Cov.: 22

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0944

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.000858

Gnomad SAS AF: 0.0530

Gnomad FIN AF: 0.0564

Gnomad MID AF: 0.0720

Gnomad NFE AF: 0.0712

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0871 AC: 9644 AN: 110684 Hom.: 410 Cov.: 22 AF XY: 0.0790 AC XY: 2611 AN XY: 33058

African (AFR) AF: 0.156 AC: 4752 AN: 30462

American (AMR) AF: 0.0420 AC: 437 AN: 10412

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 63 AN: 2636

East Asian (EAS) AF: 0.000860 AC: 3 AN: 3488

South Asian (SAS) AF: 0.0536 AC: 141 AN: 2633

European-Finnish (FIN) AF: 0.0564 AC: 335 AN: 5938

Middle Eastern (MID) AF: 0.0744 AC: 16 AN: 215

European-Non Finnish (NFE) AF: 0.0712 AC: 3751 AN: 52706

Other (OTH) AF: 0.0541 AC: 82 AN: 1516

Alfa AF: 0.0751 Hom.: 2548

Bravo AF: 0.0889

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.42
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs1397631; hg19: chrX-66352696;