rs6618677

Variant names:

• chrX-91557719-A-G
• rs6618677

Your query was ambiguous. Multiple possible variants found:

• chrX-91557719-A-G
• chrX-91557719-A-T

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 0.2 in 111,268 control chromosomes in the GnomAD database, including 1,648 homozygotes. There are 6,741 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 0.20 (1648 hom., 6741 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 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: 0.200 AC: 22262 AN: 111216 Hom.: 1640 Cov.: 23

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.151

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.200 AC: 22289 AN: 111268 Hom.: 1648 Cov.: 23 AF XY: 0.201 AC XY: 6741 AN XY: 33524

African (AFR) AF: 0.167 AC: 5146 AN: 30801

American (AMR) AF: 0.283 AC: 2943 AN: 10415

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 382 AN: 2641

East Asian (EAS) AF: 0.314 AC: 1109 AN: 3532

South Asian (SAS) AF: 0.213 AC: 566 AN: 2652

European-Finnish (FIN) AF: 0.281 AC: 1659 AN: 5898

Middle Eastern (MID) AF: 0.147 AC: 32 AN: 218

European-Non Finnish (NFE) AF: 0.190 AC: 10070 AN: 52928

Other (OTH) AF: 0.200 AC: 301 AN: 1503

Alfa AF: 0.121 Hom.: 650

Bravo AF: 0.206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	8.4
DANN	Benign	0.93
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs6618677; hg19: chrX-90812718;