5-150157631-A-G

Variant names:

• chr5-150157631-A-G
• rs3756312

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 0.422 in 151,928 control chromosomes in the GnomAD database, including 15,278 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 0.42 (15278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 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: 0.422 AC: 64015 AN: 151808 Hom.: 15245 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.422 AC: 64109 AN: 151928 Hom.: 15278 Cov.: 32 AF XY: 0.420 AC XY: 31188 AN XY: 74240

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.441

Alfa AF: 0.380 Hom.: 1133

Bravo AF: 0.441

Asia WGS AF: 0.454 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3756312; hg19: chr5-149537194;