rs6654100

Variant names:

• chrX-21998020-C-A
• rs6654100

Your query was ambiguous. Multiple possible variants found:

• chrX-21998020-C-A
• chrX-21998020-C-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 0.217 in 111,394 control chromosomes in the GnomAD database, including 2,358 homozygotes. There are 6,919 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 0.22 (2358 hom., 6919 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 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: 0.217 AC: 24140 AN: 111337 Hom.: 2356 Cov.: 23

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0615

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.217 AC: 24170 AN: 111394 Hom.: 2358 Cov.: 23 AF XY: 0.206 AC XY: 6919 AN XY: 33622

African (AFR) AF: 0.378 AC: 11552 AN: 30551

American (AMR) AF: 0.127 AC: 1330 AN: 10488

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 407 AN: 2642

East Asian (EAS) AF: 0.136 AC: 482 AN: 3542

South Asian (SAS) AF: 0.0610 AC: 165 AN: 2707

European-Finnish (FIN) AF: 0.173 AC: 1036 AN: 5972

Middle Eastern (MID) AF: 0.152 AC: 33 AN: 217

European-Non Finnish (NFE) AF: 0.165 AC: 8752 AN: 53081

Other (OTH) AF: 0.194 AC: 296 AN: 1522

Alfa AF: 0.0731 Hom.: 338

Bravo AF: 0.224

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.2
DANN	Benign	0.76
PhyloP100		0.089
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6654100; hg19: chrX-22016138; COSMIC: COSV65115559;