3-80377418-A-C

Variant names:

• chr3-80377418-A-C
• rs949455

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.152 in 152,092 control chromosomes in the GnomAD database, including 3,025 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 0.15 (3025 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 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: 0.152 AC: 23121 AN: 151974 Hom.: 3019 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0631

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0528

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.152 AC: 23165 AN: 152092 Hom.: 3025 Cov.: 32 AF XY: 0.156 AC XY: 11590 AN XY: 74368

African (AFR) AF: 0.296 AC: 12253 AN: 41428

American (AMR) AF: 0.172 AC: 2637 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3470

East Asian (EAS) AF: 0.532 AC: 2746 AN: 5166

South Asian (SAS) AF: 0.155 AC: 747 AN: 4824

European-Finnish (FIN) AF: 0.0631 AC: 668 AN: 10594

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0528 AC: 3589 AN: 68006

Other (OTH) AF: 0.132 AC: 279 AN: 2110

Alfa AF: 0.0628 Hom.: 244

Bravo AF: 0.169

Asia WGS AF: 0.287 AC: 997 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	0.86
DANN	Benign	0.68
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs949455; hg19: chr3-80426568;