rs6626055

Variant names:

• chrX-144544485-A-C
• rs6626055

Your query was ambiguous. Multiple possible variants found:

• chrX-144544485-A-C
• chrX-144544485-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 0.0244 in 111,088 control chromosomes in the GnomAD database, including 84 homozygotes. There are 812 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 0.024 (84 hom., 812 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 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: 0.0245 AC: 2717 AN: 111038 Hom.: 85 Cov.: 22

Gnomad AFR AF: 0.00434

Gnomad AMI AF: 0.0250

Gnomad AMR AF: 0.0119

Gnomad ASJ AF: 0.00607

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.0747

Gnomad FIN AF: 0.0141

Gnomad MID AF: 0.00844

Gnomad NFE AF: 0.0259

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0244 AC: 2712 AN: 111088 Hom.: 84 Cov.: 22 AF XY: 0.0243 AC XY: 812 AN XY: 33374

African (AFR) AF: 0.00433 AC: 133 AN: 30741

American (AMR) AF: 0.0119 AC: 123 AN: 10379

Ashkenazi Jewish (ASJ) AF: 0.00607 AC: 16 AN: 2634

East Asian (EAS) AF: 0.212 AC: 734 AN: 3455

South Asian (SAS) AF: 0.0742 AC: 198 AN: 2667

European-Finnish (FIN) AF: 0.0141 AC: 84 AN: 5963

Middle Eastern (MID) AF: 0.00463 AC: 1 AN: 216

European-Non Finnish (NFE) AF: 0.0259 AC: 1370 AN: 52837

Other (OTH) AF: 0.0237 AC: 36 AN: 1516

Alfa AF: 0.0221 Hom.: 807

Bravo AF: 0.0245

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.63
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs6626055; hg19: chrX-143626006;