8-13682492-T-C

Variant names:

• chr8-13682492-T-C
• rs4831455

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 0.289 in 151,868 control chromosomes in the GnomAD database, including 6,598 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 0.29 (6598 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43835 AN: 151750 Hom.: 6592 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.289 AC: 43858 AN: 151868 Hom.: 6598 Cov.: 32 AF XY: 0.288 AC XY: 21382 AN XY: 74208

African (AFR) AF: 0.333 AC: 13800 AN: 41418

American (AMR) AF: 0.230 AC: 3503 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 729 AN: 3462

East Asian (EAS) AF: 0.208 AC: 1071 AN: 5158

South Asian (SAS) AF: 0.420 AC: 2025 AN: 4820

European-Finnish (FIN) AF: 0.237 AC: 2505 AN: 10550

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19448 AN: 67944

Other (OTH) AF: 0.268 AC: 564 AN: 2108

Alfa AF: 0.274 Hom.: 7465

Bravo AF: 0.284

Asia WGS AF: 0.338 AC: 1174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs4831455; hg19: chr8-13540001;