rs7432089

chr3-162592214-C-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 0.535 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

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 (EAS) allele frequency at 95% confidence interval = 0.647 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: 0.535 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

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.484

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7432089; hg19: chr3-162310002;