rs1601226

Positions:

• chrX-127345795-G-A
• chrX-127345795-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0485 AC: 5290 AN: 109094 Hom.: 287 Cov.: 22 AF XY: 0.0432 AC XY: 1391 AN XY: 32174

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

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0203

Gnomad4 ASJ AF: 0.0218

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00151

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000590

Gnomad4 OTH AF: 0.0479

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1601226; hg19: chrX-126479778;