rs149910

Variant names:

• chrX-127191155-G-T
• rs149910

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 0.398 in 110,468 control chromosomes in the GnomAD database, including 6,641 homozygotes. There are 13,200 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 0.40 (6641 hom., 13200 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 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: 0.398 AC: 43964 AN: 110413 Hom.: 6643 Cov.: 22

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.398 AC: 43986 AN: 110468 Hom.: 6641 Cov.: 22 AF XY: 0.403 AC XY: 13200 AN XY: 32788

African (AFR) AF: 0.530 AC: 16145 AN: 30475

American (AMR) AF: 0.439 AC: 4541 AN: 10334

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 699 AN: 2639

East Asian (EAS) AF: 0.593 AC: 2033 AN: 3426

South Asian (SAS) AF: 0.480 AC: 1287 AN: 2680

European-Finnish (FIN) AF: 0.424 AC: 2467 AN: 5820

Middle Eastern (MID) AF: 0.274 AC: 58 AN: 212

European-Non Finnish (NFE) AF: 0.303 AC: 15989 AN: 52703

Other (OTH) AF: 0.386 AC: 581 AN: 1506

Alfa AF: 0.359 Hom.: 2784

Bravo AF: 0.409

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.095
DANN	Benign	0.48
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs149910; hg19: chrX-126325138;