3-96448764-T-G

Variant names:

• chr3-96448764-T-G
• rs326254

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 0.595 in 151,312 control chromosomes in the GnomAD database, including 28,311 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 0.60 (28311 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.644
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 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: 0.596 AC: 90043 AN: 151196 Hom.: 28314 Cov.: 28

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.595 AC: 90049 AN: 151312 Hom.: 28311 Cov.: 28 AF XY: 0.595 AC XY: 43956 AN XY: 73850

African (AFR) AF: 0.369 AC: 15196 AN: 41192

American (AMR) AF: 0.620 AC: 9406 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2453 AN: 3466

East Asian (EAS) AF: 0.777 AC: 3956 AN: 5092

South Asian (SAS) AF: 0.736 AC: 3514 AN: 4776

European-Finnish (FIN) AF: 0.636 AC: 6630 AN: 10428

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46816 AN: 67872

Other (OTH) AF: 0.634 AC: 1331 AN: 2098

Alfa AF: 0.616 Hom.: 4942

Bravo AF: 0.582

Asia WGS AF: 0.737 AC: 2552 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.6
DANN	Benign	0.69
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs326254; hg19: chr3-96167608;