chr3-36313045-A-C

Position:

• chr3-36313045-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 0.859 in 152,132 control chromosomes in the GnomAD database, including 56,154 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 0.86 (56154 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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: 0.859 AC: 130517 AN: 152016 Hom.: 56110 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.859 AC: 130620 AN: 152132 Hom.: 56154 Cov.: 32 AF XY: 0.863 AC XY: 64158 AN XY: 74376

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.895

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.840

Alfa AF: 0.839 Hom.: 20805

Bravo AF: 0.855

Asia WGS AF: 0.925 AC: 3216 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	2.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1871352; hg19: chr3-36354537;