X-67736589-T-C

Variant names:

• chrX-67736589-T-C
• rs5964607

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 0.618 in 111,046 control chromosomes in the GnomAD database, including 18,275 homozygotes. There are 21,048 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 (18275 hom., 21048 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 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: 0.619 AC: 68663 AN: 110989 Hom.: 18283 Cov.: 23

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.657

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.618 AC: 68655 AN: 111046 Hom.: 18275 Cov.: 23 AF XY: 0.632 AC XY: 21048 AN XY: 33292

African (AFR) AF: 0.130 AC: 4015 AN: 30838

American (AMR) AF: 0.789 AC: 8196 AN: 10388

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2096 AN: 2624

East Asian (EAS) AF: 0.996 AC: 3484 AN: 3497

South Asian (SAS) AF: 0.902 AC: 2318 AN: 2571

European-Finnish (FIN) AF: 0.819 AC: 4864 AN: 5937

Middle Eastern (MID) AF: 0.637 AC: 137 AN: 215

European-Non Finnish (NFE) AF: 0.795 AC: 41972 AN: 52800

Other (OTH) AF: 0.656 AC: 984 AN: 1501

Alfa AF: 0.757 Hom.: 23723

Bravo AF: 0.603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.37
DANN	Benign	0.65
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs5964607; hg19: chrX-66956431;