rs5970164

Variant names:

• chrX-151930634-C-T
• rs5970164

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 0.212 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.212 AC: 23242 AN: 109567 Hom.: 2498 Cov.: 22

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

African (AFR) AF: 0.423 AC: 12690 AN: 30023

American (AMR) AF: 0.129 AC: 1328 AN: 10300

Ashkenazi Jewish (ASJ) AF: 0.0923 AC: 242 AN: 2621

East Asian (EAS) AF: 0.0106 AC: 37 AN: 3493

South Asian (SAS) AF: 0.178 AC: 452 AN: 2534

European-Finnish (FIN) AF: 0.198 AC: 1141 AN: 5768

Middle Eastern (MID) AF: 0.129 AC: 27 AN: 209

European-Non Finnish (NFE) AF: 0.132 AC: 6957 AN: 52509

Other (OTH) AF: 0.199 AC: 296 AN: 1488

Alfa AF: 0.172 Hom.: 12764

Bravo AF: 0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.40
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs5970164; hg19: chrX-151099106;