chr8-53253159-C-T

Variant names:

• chr8-53253159-C-T
• rs35970029

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 0.0507 in 152,200 control chromosomes in the GnomAD database, including 293 homozygotes. 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 0.051 (293 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.157 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: 0.0508 AC: 7723 AN: 152082 Hom.: 292 Cov.: 32

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0293

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0833

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0423

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0507 AC: 7723 AN: 152200 Hom.: 293 Cov.: 32 AF XY: 0.0552 AC XY: 4109 AN XY: 74380

African (AFR) AF: 0.0358 AC: 1486 AN: 41538

American (AMR) AF: 0.0292 AC: 447 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 309 AN: 3472

East Asian (EAS) AF: 0.167 AC: 862 AN: 5172

South Asian (SAS) AF: 0.150 AC: 723 AN: 4808

European-Finnish (FIN) AF: 0.0833 AC: 881 AN: 10572

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0423 AC: 2879 AN: 68018

Other (OTH) AF: 0.0521 AC: 110 AN: 2112

Alfa AF: 0.0488 Hom.: 29

Bravo AF: 0.0448

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.5
DANN	Benign	0.74
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs35970029; hg19: chr8-54165719;