chr3-136237463-A-C

Variant names:

• chr3-136237463-A-C
• rs684773

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;