X-67744643-G-A

Variant names:

• chrX-67744643-G-A
• rs1415270

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 0.619 in 110,865 control chromosomes in the GnomAD database, including 18,291 homozygotes. There are 21,023 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 0.62 (18291 hom., 21023 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.620 AC: 68668 AN: 110810 Hom.: 18299 Cov.: 23

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.619 AC: 68662 AN: 110865 Hom.: 18291 Cov.: 23 AF XY: 0.635 AC XY: 21023 AN XY: 33101

African (AFR) AF: 0.130 AC: 3972 AN: 30631

American (AMR) AF: 0.789 AC: 8211 AN: 10412

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2090 AN: 2625

East Asian (EAS) AF: 0.998 AC: 3475 AN: 3482

South Asian (SAS) AF: 0.902 AC: 2312 AN: 2564

European-Finnish (FIN) AF: 0.821 AC: 4815 AN: 5865

Middle Eastern (MID) AF: 0.638 AC: 136 AN: 213

European-Non Finnish (NFE) AF: 0.795 AC: 42060 AN: 52881

Other (OTH) AF: 0.658 AC: 994 AN: 1510

Alfa AF: 0.765 Hom.: 21366

Bravo AF: 0.603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.31
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1415270; hg19: chrX-66964485;