rs72619425

Positions:

• chrX-37753178-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 0.207 in 110,348 control chromosomes in the GnomAD database, including 1,972 homozygotes. There are 6,420 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 0.21 (1972 hom., 6420 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.207 AC: 22795 AN: 110294 Hom.: 1969 Cov.: 22 AF XY: 0.196 AC XY: 6400 AN XY: 32588

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0698

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.207 AC: 22817 AN: 110348 Hom.: 1972 Cov.: 22 AF XY: 0.197 AC XY: 6420 AN XY: 32652

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.0691

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.183

Alfa AF: 0.213 Hom.: 1295

Bravo AF: 0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs72619425; hg19: chrX-37612431;