5-153260117-A-G

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/exons	MANE	UniProt

Ensembl

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