rs3116136

Variant names:

• chr8-73001513-G-C
• rs3116136

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 0.2 in 152,080 control chromosomes in the GnomAD database, including 3,149 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 0.20 (3149 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 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: 0.200 AC: 30392 AN: 151962 Hom.: 3149 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.200 AC: 30406 AN: 152080 Hom.: 3149 Cov.: 32 AF XY: 0.196 AC XY: 14584 AN XY: 74338

African (AFR) AF: 0.151 AC: 6271 AN: 41496

American (AMR) AF: 0.177 AC: 2704 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1059 AN: 3468

East Asian (EAS) AF: 0.153 AC: 794 AN: 5174

South Asian (SAS) AF: 0.224 AC: 1076 AN: 4814

European-Finnish (FIN) AF: 0.159 AC: 1680 AN: 10572

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16044 AN: 67956

Other (OTH) AF: 0.214 AC: 452 AN: 2110

Alfa AF: 0.212 Hom.: 487

Bravo AF: 0.197

Asia WGS AF: 0.178 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.54
DANN	Benign	0.39
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs3116136; hg19: chr8-73913748;