3-46350297-T-G

Variant names:

• chr3-46350297-T-G
• rs17141006

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 0.132 in 152,270 control chromosomes in the GnomAD database, including 1,569 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 0.13 (1569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 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: 0.132 AC: 20116 AN: 152152 Hom.: 1562 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0633

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0902

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.132 AC: 20151 AN: 152270 Hom.: 1569 Cov.: 32 AF XY: 0.133 AC XY: 9920 AN XY: 74460

African (AFR) AF: 0.195 AC: 8086 AN: 41534

American (AMR) AF: 0.176 AC: 2687 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3472

East Asian (EAS) AF: 0.212 AC: 1095 AN: 5174

South Asian (SAS) AF: 0.124 AC: 597 AN: 4828

European-Finnish (FIN) AF: 0.0633 AC: 672 AN: 10618

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0902 AC: 6133 AN: 68018

Other (OTH) AF: 0.137 AC: 289 AN: 2116

Alfa AF: 0.107 Hom.: 1386

Bravo AF: 0.145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.55
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs17141006; hg19: chr3-46391788;