8-116583784-T-G

Variant names:

• chr8-116583784-T-G
• rs13249356

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 0.187 in 152,232 control chromosomes in the GnomAD database, including 3,139 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 0.19 (3139 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28380 AN: 152114 Hom.: 3137 Cov.: 32

Gnomad AFR AF: 0.0930

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.187 AC: 28401 AN: 152232 Hom.: 3139 Cov.: 32 AF XY: 0.190 AC XY: 14106 AN XY: 74434

African (AFR) AF: 0.0932 AC: 3872 AN: 41560

American (AMR) AF: 0.261 AC: 3994 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1014 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2506 AN: 5178

South Asian (SAS) AF: 0.287 AC: 1382 AN: 4816

European-Finnish (FIN) AF: 0.168 AC: 1784 AN: 10608

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13267 AN: 67994

Other (OTH) AF: 0.200 AC: 422 AN: 2114

Alfa AF: 0.192 Hom.: 488

Bravo AF: 0.186

Asia WGS AF: 0.327 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	15
DANN	Benign	0.61
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs13249356; hg19: chr8-117596023;