rs7061267

Variant names:

• chrX-891644-T-C
• rs7061267

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.0905 AC: 3754 AN: 41496

American (AMR) AF: 0.0649 AC: 990 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3468

East Asian (EAS) AF: 0.0205 AC: 106 AN: 5162

South Asian (SAS) AF: 0.0962 AC: 463 AN: 4812

European-Finnish (FIN) AF: 0.0536 AC: 567 AN: 10584

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0708 AC: 4808 AN: 67956

Other (OTH) AF: 0.0782 AC: 165 AN: 2110

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
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs7061267; hg19: chrX-852379;