X-95859612-C-T

Variant names:

• chrX-95859612-C-T
• rs1857602

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 0.385 in 109,010 control chromosomes in the GnomAD database, including 6,921 homozygotes. There are 11,942 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 0.39 (6921 hom., 11942 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 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: 0.385 AC: 41948 AN: 108965 Hom.: 6920 Cov.: 22

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.385 AC: 41989 AN: 109010 Hom.: 6921 Cov.: 22 AF XY: 0.378 AC XY: 11942 AN XY: 31586

African (AFR) AF: 0.620 AC: 18689 AN: 30132

American (AMR) AF: 0.464 AC: 4707 AN: 10144

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 716 AN: 2614

East Asian (EAS) AF: 0.210 AC: 726 AN: 3449

South Asian (SAS) AF: 0.253 AC: 655 AN: 2591

European-Finnish (FIN) AF: 0.317 AC: 1794 AN: 5665

Middle Eastern (MID) AF: 0.318 AC: 64 AN: 201

European-Non Finnish (NFE) AF: 0.269 AC: 13982 AN: 52059

Other (OTH) AF: 0.354 AC: 522 AN: 1476

Alfa AF: 0.284 Hom.: 15745

Bravo AF: 0.415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.20
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1857602; hg19: chrX-95114611; COSMIC: COSV70048366;