rs7432089

Variant names:

• chr3-162592214-C-G
• rs7432089

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 0.535 in 151,710 control chromosomes in the GnomAD database, including 22,213 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 (22213 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.647 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: 0.535 AC: 81097 AN: 151592 Hom.: 22180 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.535 AC: 81172 AN: 151710 Hom.: 22213 Cov.: 31 AF XY: 0.537 AC XY: 39855 AN XY: 74154

African (AFR) AF: 0.644 AC: 26645 AN: 41398

American (AMR) AF: 0.477 AC: 7273 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1481 AN: 3460

East Asian (EAS) AF: 0.666 AC: 3434 AN: 5156

South Asian (SAS) AF: 0.594 AC: 2862 AN: 4822

European-Finnish (FIN) AF: 0.516 AC: 5439 AN: 10538

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32479 AN: 67774

Other (OTH) AF: 0.484 AC: 1020 AN: 2106

Alfa AF: 0.514 Hom.: 2508

Bravo AF: 0.530

Asia WGS AF: 0.619 AC: 2153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.29
DANN	Benign	0.63
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs7432089; hg19: chr3-162310002;