rs3776082

Variant names:

• chr5-150164482-G-A
• rs3776082

Your query was ambiguous. Multiple possible variants found:

• chr5-150164482-G-A
• chr5-150164482-G-C
• chr5-150164482-G-T

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 0.482 in 151,816 control chromosomes in the GnomAD database, including 17,954 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 0.48 (17954 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 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: 0.482 AC: 73124 AN: 151698 Hom.: 17930 Cov.: 31

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.482 AC: 73189 AN: 151816 Hom.: 17954 Cov.: 31 AF XY: 0.479 AC XY: 35542 AN XY: 74192

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.508

Alfa AF: 0.455 Hom.: 20445

Bravo AF: 0.488

Asia WGS AF: 0.505 AC: 1758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.46
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3776082; hg19: chr5-149544045;