5-153260117-A-G

Variant names:

• chr5-153260117-A-G
• rs3112530

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.416 AC: 17211 AN: 41372

American (AMR) AF: 0.862 AC: 13120 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3121 AN: 3468

East Asian (EAS) AF: 0.708 AC: 3656 AN: 5164

South Asian (SAS) AF: 0.908 AC: 4376 AN: 4820

European-Finnish (FIN) AF: 0.918 AC: 9704 AN: 10568

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.924 AC: 62704 AN: 67856

Other (OTH) AF: 0.777 AC: 1637 AN: 2106

Alfa AF: 0.861 Hom.: 100357

Bravo AF: 0.745

Asia WGS AF: 0.773 AC: 2687 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.23
PhyloP100		-0.50

Splicing

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

Other links and lift over

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