5-153260117-A-G

Variant names:

• chr5-153260117-A-G
• rs3112530

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 0.768 in 151,772 control chromosomes in the GnomAD database, including 48,581 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 0.77 (48581 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.918 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: 0.769 AC: 116578 AN: 151654 Hom.: 48576 Cov.: 31

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.924

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.768 AC: 116617 AN: 151772 Hom.: 48581 Cov.: 31 AF XY: 0.772 AC XY: 57267 AN XY: 74200

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.900

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.924

Gnomad4 OTH AF: 0.777

Alfa AF: 0.903 Hom.: 57611

Bravo AF: 0.745

Asia WGS AF: 0.773 AC: 2687 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3112530; hg19: chr5-152639677; COSMIC: COSV60214316;