3-46336534-C-T

Variant names:

• chr3-46336534-C-T
• rs2097282

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 0.68 in 151,900 control chromosomes in the GnomAD database, including 35,175 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 0.68 (35175 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 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: 0.680 AC: 103242 AN: 151782 Hom.: 35135 Cov.: 30

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.680 AC: 103323 AN: 151900 Hom.: 35175 Cov.: 30 AF XY: 0.678 AC XY: 50322 AN XY: 74234

African (AFR) AF: 0.669 AC: 27685 AN: 41396

American (AMR) AF: 0.646 AC: 9861 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2539 AN: 3468

East Asian (EAS) AF: 0.690 AC: 3557 AN: 5152

South Asian (SAS) AF: 0.644 AC: 3102 AN: 4820

European-Finnish (FIN) AF: 0.709 AC: 7479 AN: 10546

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46880 AN: 67948

Other (OTH) AF: 0.666 AC: 1405 AN: 2110

Alfa AF: 0.646 Hom.: 2180

Bravo AF: 0.677

Asia WGS AF: 0.692 AC: 2406 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.25
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2097282; hg19: chr3-46378025;