rs2382932

Variant names:

• chrX-144819086-A-C
• rs2382932

Your query was ambiguous. Multiple possible variants found:

• chrX-144819086-A-C
• chrX-144819086-A-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 0.482 in 109,255 control chromosomes in the GnomAD database, including 10,167 homozygotes. There are 14,848 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 0.48 (10167 hom., 14848 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 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: 0.482 AC: 52606 AN: 109210 Hom.: 10166 Cov.: 22 AF XY: 0.464 AC XY: 14801 AN XY: 31880

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.482 AC: 52645 AN: 109255 Hom.: 10167 Cov.: 22 AF XY: 0.465 AC XY: 14848 AN XY: 31935

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.523

Alfa AF: 0.416 Hom.: 10447

Bravo AF: 0.515

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.17
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2382932; hg19: chrX-143900607;