chr5-132033548-A-G

Variant names:

• chr5-132033548-A-G
• rs3916441

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 0.543 in 151,856 control chromosomes in the GnomAD database, including 22,938 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 0.54 (22938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.01
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 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: 0.543 AC: 82333 AN: 151738 Hom.: 22917 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.543 AC: 82401 AN: 151856 Hom.: 22938 Cov.: 32 AF XY: 0.534 AC XY: 39642 AN XY: 74212

African (AFR) AF: 0.656 AC: 27183 AN: 41444

American (AMR) AF: 0.494 AC: 7539 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1661 AN: 3472

East Asian (EAS) AF: 0.541 AC: 2794 AN: 5164

South Asian (SAS) AF: 0.322 AC: 1555 AN: 4822

European-Finnish (FIN) AF: 0.474 AC: 4994 AN: 10528

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.515 AC: 34911 AN: 67852

Other (OTH) AF: 0.538 AC: 1133 AN: 2106

Alfa AF: 0.515 Hom.: 27980

Bravo AF: 0.555

Asia WGS AF: 0.450 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.21
DANN	Benign	0.22
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs3916441; hg19: chr5-131369241;