rs2128990

Variant names:

• chrX-150935362-G-A
• rs2128990

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 0.243 in 111,036 control chromosomes in the GnomAD database, including 2,537 homozygotes. There are 7,974 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 0.24 (2537 hom., 7974 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.414 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: 0.243 AC: 26926 AN: 110982 Hom.: 2531 Cov.: 23

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.230

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.243 AC: 26950 AN: 111036 Hom.: 2537 Cov.: 23 AF XY: 0.240 AC XY: 7974 AN XY: 33246

African (AFR) AF: 0.263 AC: 8025 AN: 30560

American (AMR) AF: 0.425 AC: 4415 AN: 10397

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 677 AN: 2641

East Asian (EAS) AF: 0.245 AC: 861 AN: 3509

South Asian (SAS) AF: 0.194 AC: 514 AN: 2651

European-Finnish (FIN) AF: 0.231 AC: 1359 AN: 5888

Middle Eastern (MID) AF: 0.234 AC: 50 AN: 214

European-Non Finnish (NFE) AF: 0.198 AC: 10468 AN: 52978

Other (OTH) AF: 0.277 AC: 421 AN: 1522

Alfa AF: 0.226 Hom.: 22009

Bravo AF: 0.264

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.45
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs2128990; hg19: chrX-150103835;