chr3-136232079-A-G

Variant names:

• chr3-136232079-A-G
• rs511154

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 0.753 in 151,812 control chromosomes in the GnomAD database, including 43,387 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 0.75 (43387 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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: 0.753 AC: 114211 AN: 151696 Hom.: 43354 Cov.: 29

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.753 AC: 114299 AN: 151812 Hom.: 43387 Cov.: 29 AF XY: 0.758 AC XY: 56209 AN XY: 74154

African (AFR) AF: 0.661 AC: 27324 AN: 41316

American (AMR) AF: 0.780 AC: 11864 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2420 AN: 3464

East Asian (EAS) AF: 0.863 AC: 4465 AN: 5174

South Asian (SAS) AF: 0.816 AC: 3923 AN: 4808

European-Finnish (FIN) AF: 0.864 AC: 9115 AN: 10550

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52833 AN: 67978

Other (OTH) AF: 0.738 AC: 1555 AN: 2106

Alfa AF: 0.963 Hom.: 56804

Bravo AF: 0.741

Asia WGS AF: 0.832 AC: 2891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.57
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs511154; hg19: chr3-135950921;