3-46304534-T-G

Variant names:

• chr3-46304534-T-G
• rs10510751

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 0.122 in 152,232 control chromosomes in the GnomAD database, including 1,316 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 0.12 (1316 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18589 AN: 152114 Hom.: 1310 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.0613

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0880

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.122 AC: 18620 AN: 152232 Hom.: 1316 Cov.: 33 AF XY: 0.123 AC XY: 9126 AN XY: 74442

African (AFR) AF: 0.167 AC: 6935 AN: 41534

American (AMR) AF: 0.177 AC: 2708 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3472

East Asian (EAS) AF: 0.205 AC: 1065 AN: 5184

South Asian (SAS) AF: 0.0880 AC: 425 AN: 4828

European-Finnish (FIN) AF: 0.0613 AC: 650 AN: 10610

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0880 AC: 5985 AN: 67988

Other (OTH) AF: 0.139 AC: 295 AN: 2116

Alfa AF: 0.102 Hom.: 2148

Bravo AF: 0.135

Asia WGS AF: 0.170 AC: 590 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.31
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs10510751; hg19: chr3-46346025;