rs1397631

chrX-67132854-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0872 AC: 9643 AN: 110634 Hom.: 411 Cov.: 22 AF XY: 0.0792 AC XY: 2614 AN XY: 32998

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

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.0420

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.000860

Gnomad4 SAS AF: 0.0536

Gnomad4 FIN AF: 0.0564

Gnomad4 NFE AF: 0.0712

Gnomad4 OTH AF: 0.0541

Alfa AF: 0.0716 Hom.: 1292

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1397631; hg19: chrX-66352696;