rs1601226

Variant names:

• chrX-127345795-G-A
• rs1601226

Your query was ambiguous. Multiple possible variants found:

• chrX-127345795-G-A
• chrX-127345795-G-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 0.0486 in 109,122 control chromosomes in the GnomAD database, including 286 homozygotes. There are 1,398 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 0.049 (286 hom., 1398 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.805
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 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: 0.0485 AC: 5290 AN: 109094 Hom.: 287 Cov.: 22

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0203

Gnomad ASJ AF: 0.0218

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00150

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0218

Gnomad NFE AF: 0.000590

Gnomad OTH AF: 0.0485

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

GnomAD4 genome AF: 0.0486 AC: 5298 AN: 109122 Hom.: 286 Cov.: 22 AF XY: 0.0434 AC XY: 1398 AN XY: 32214

African (AFR) AF: 0.163 AC: 4921 AN: 30124

American (AMR) AF: 0.0203 AC: 208 AN: 10260

Ashkenazi Jewish (ASJ) AF: 0.0218 AC: 57 AN: 2620

East Asian (EAS) AF: 0.00 AC: 0 AN: 3477

South Asian (SAS) AF: 0.00151 AC: 4 AN: 2647

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5097

Middle Eastern (MID) AF: 0.0243 AC: 5 AN: 206

European-Non Finnish (NFE) AF: 0.000590 AC: 31 AN: 52508

Other (OTH) AF: 0.0479 AC: 72 AN: 1503

Alfa AF: 0.00144 Hom.: 7

Bravo AF: 0.0564

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.35
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs1601226; hg19: chrX-126479778;