rs5970164

Positions:

• chrX-151930634-C-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 0.212 in 109,615 control chromosomes in the GnomAD database, including 2,495 homozygotes. There are 6,587 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 0.21 (2495 hom., 6587 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 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: 0.212 AC: 23242 AN: 109567 Hom.: 2498 Cov.: 22 AF XY: 0.204 AC XY: 6566 AN XY: 32145

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0923

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.212 AC: 23260 AN: 109615 Hom.: 2495 Cov.: 22 AF XY: 0.205 AC XY: 6587 AN XY: 32203

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0923

Gnomad4 EAS AF: 0.0106

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.199

Alfa AF: 0.150 Hom.: 7802

Bravo AF: 0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5970164; hg19: chrX-151099106;