3-96448764-T-G

Variant names:

• chr3-96448764-T-G
• rs326254

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 0.595 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.634

Alfa AF: 0.624 Hom.: 4885

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs326254; hg19: chr3-96167608;