chr5-150164482-G-A

Position:

• chr5-150164482-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 0.482 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;