3-55465636-G-A

Position:

• chr3-55465636-G-A

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 0.438 in 151,964 control chromosomes in the GnomAD database, including 15,132 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 0.44 (15132 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.507

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66570 AN: 151846 Hom.: 15125 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.438 AC: 66585 AN: 151964 Hom.: 15132 Cov.: 32 AF XY: 0.438 AC XY: 32547 AN XY: 74260

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.454

Alfa AF: 0.456 Hom.: 16044

Bravo AF: 0.451

Asia WGS AF: 0.494 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12497254; hg19: chr3-55499664;