3-46304534-T-G

Variant names:

• chr3-46304534-T-G
• rs10510751

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 0.122 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.122 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

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.0880

Gnomad4 FIN AF: 0.0613

Gnomad4 NFE AF: 0.0880

Gnomad4 OTH AF: 0.139

Alfa AF: 0.0988 Hom.: 1302

Bravo AF: 0.135

Asia WGS AF: 0.170 AC: 590 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510751; hg19: chr3-46346025;