3-136237463-A-C

Position:

• chr3-136237463-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.794 in 151,906 control chromosomes in the GnomAD database, including 47,954 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 0.79 (47954 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120463 AN: 151788 Hom.: 47900 Cov.: 31

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.794 AC: 120579 AN: 151906 Hom.: 47954 Cov.: 31 AF XY: 0.798 AC XY: 59219 AN XY: 74252

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.772

Alfa AF: 0.779 Hom.: 23276

Bravo AF: 0.787

Asia WGS AF: 0.847 AC: 2944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs684773; hg19: chr3-135956305;