rs7061267

Positions:

• chrX-891644-T-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 0.0738 in 152,060 control chromosomes in the GnomAD database, including 469 homozygotes. There are 5,383 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 0.074 (469 hom., 5383 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

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 (SAS) allele frequency at 95% confidence interval = 0.089 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: 0.0737 AC: 11197 AN: 151940 Hom.: 466 Cov.: 31 AF XY: 0.0723 AC XY: 5363 AN XY: 74204

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0649

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.0201

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.0536

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.0790

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

GnomAD4 genome AF: 0.0738 AC: 11219 AN: 152060 Hom.: 469 Cov.: 31 AF XY: 0.0724 AC XY: 5383 AN XY: 74334

Gnomad4 AFR AF: 0.0905

Gnomad4 AMR AF: 0.0649

Gnomad4 ASJ AF: 0.0732

Gnomad4 EAS AF: 0.0205

Gnomad4 SAS AF: 0.0962

Gnomad4 FIN AF: 0.0536

Gnomad4 NFE AF: 0.0708

Gnomad4 OTH AF: 0.0782

Bravo AF: 0.0739

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.097

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7061267; hg19: chrX-852379;