chr3-46324778-A-G

Position:

• chr3-46324778-A-G

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 0.736 in 152,176 control chromosomes in the GnomAD database, including 41,618 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 0.74 (41618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 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: 0.736 AC: 111869 AN: 152058 Hom.: 41558 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.736 AC: 111981 AN: 152176 Hom.: 41618 Cov.: 32 AF XY: 0.732 AC XY: 54457 AN XY: 74402

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.716

Alfa AF: 0.729 Hom.: 9435

Bravo AF: 0.743

Asia WGS AF: 0.712 AC: 2477 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2157057; hg19: chr3-46366269;