3-32900360-G-T

Variant names:

• chr3-32900360-G-T
• rs7648704

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 0.623 in 151,978 control chromosomes in the GnomAD database, including 29,959 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 0.62 (29959 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 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: 0.623 AC: 94577 AN: 151860 Hom.: 29942 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.623 AC: 94638 AN: 151978 Hom.: 29959 Cov.: 31 AF XY: 0.625 AC XY: 46440 AN XY: 74258

African (AFR) AF: 0.497 AC: 20598 AN: 41420

American (AMR) AF: 0.684 AC: 10438 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2404 AN: 3470

East Asian (EAS) AF: 0.761 AC: 3925 AN: 5156

South Asian (SAS) AF: 0.713 AC: 3439 AN: 4822

European-Finnish (FIN) AF: 0.642 AC: 6778 AN: 10556

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45036 AN: 67970

Other (OTH) AF: 0.643 AC: 1357 AN: 2110

Alfa AF: 0.644 Hom.: 56489

Bravo AF: 0.621

Asia WGS AF: 0.740 AC: 2574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.16
DANN	Benign	0.84
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7648704; hg19: chr3-32941852;