8-100915467-C-T

Variant names:

• chr8-100915467-C-T
• rs13254653

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 0.367 in 152,034 control chromosomes in the GnomAD database, including 10,747 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 0.37 (10747 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 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: 0.367 AC: 55770 AN: 151916 Hom.: 10707 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.367 AC: 55862 AN: 152034 Hom.: 10747 Cov.: 32 AF XY: 0.361 AC XY: 26852 AN XY: 74316

African (AFR) AF: 0.463 AC: 19192 AN: 41458

American (AMR) AF: 0.323 AC: 4939 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3468

East Asian (EAS) AF: 0.150 AC: 778 AN: 5178

South Asian (SAS) AF: 0.310 AC: 1494 AN: 4816

European-Finnish (FIN) AF: 0.314 AC: 3315 AN: 10562

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23808 AN: 67954

Other (OTH) AF: 0.358 AC: 755 AN: 2110

Alfa AF: 0.351 Hom.: 29668

Bravo AF: 0.372

Asia WGS AF: 0.231 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.28
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs13254653; hg19: chr8-101927695;