rs7892772

Positions:

• chrX-71198352-G-C

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 0.145 in 110,512 control chromosomes in the GnomAD database, including 1,220 homozygotes. There are 4,492 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 0.15 (1220 hom., 4492 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 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: 0.145 AC: 16034 AN: 110459 Hom.: 1215 Cov.: 22 AF XY: 0.137 AC XY: 4483 AN XY: 32801

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0870

Gnomad SAS AF: 0.0627

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0863

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.145 AC: 16057 AN: 110512 Hom.: 1220 Cov.: 22 AF XY: 0.137 AC XY: 4492 AN XY: 32864

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.0870

Gnomad4 SAS AF: 0.0606

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.0863

Gnomad4 OTH AF: 0.126

Alfa AF: 0.117 Hom.: 645

Bravo AF: 0.154

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7892772; hg19: chrX-70418202;