rs7061267

Variant names:

• chrX-891644-T-C
• rs7061267

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;