rs985081

Variant names:

• chrX-149456568-T-C
• rs985081

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 0.145 in 111,371 control chromosomes in the GnomAD database, including 1,069 homozygotes. There are 4,547 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 0.14 (1069 hom., 4547 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 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: 0.145 AC: 16095 AN: 111313 Hom.: 1068 Cov.: 23 AF XY: 0.136 AC XY: 4540 AN XY: 33497

Gnomad AFR AF: 0.0666

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.00867

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.145 AC: 16101 AN: 111371 Hom.: 1069 Cov.: 23 AF XY: 0.135 AC XY: 4547 AN XY: 33565

Gnomad4 AFR AF: 0.0666

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.00869

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.146

Alfa AF: 0.188 Hom.: 8225

Bravo AF: 0.137

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs985081; hg19: chrX-148538099;