rs6627788

Variant names:

• chrX-153366099-G-A
• rs6627788

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 0.422 in 110,297 control chromosomes in the GnomAD database, including 8,067 homozygotes. There are 13,493 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 0.42 (8067 hom., 13493 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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: 0.422 AC: 46519 AN: 110246 Hom.: 8056 Cov.: 23

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.0805

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.422 AC: 46569 AN: 110297 Hom.: 8067 Cov.: 23 AF XY: 0.414 AC XY: 13493 AN XY: 32559

African (AFR) AF: 0.663 AC: 20044 AN: 30214

American (AMR) AF: 0.421 AC: 4334 AN: 10302

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 813 AN: 2641

East Asian (EAS) AF: 0.525 AC: 1824 AN: 3475

South Asian (SAS) AF: 0.309 AC: 813 AN: 2633

European-Finnish (FIN) AF: 0.348 AC: 2022 AN: 5808

Middle Eastern (MID) AF: 0.319 AC: 69 AN: 216

European-Non Finnish (NFE) AF: 0.302 AC: 15952 AN: 52818

Other (OTH) AF: 0.427 AC: 643 AN: 1507

Alfa AF: 0.386 Hom.: 3408

Bravo AF: 0.444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.51
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs6627788; hg19: chrX-152631557; COSMIC: COSV70114610;