3-1510024-G-A

Position:

• chr3-1510024-G-A

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 0.0882 in 151,584 control chromosomes in the GnomAD database, including 789 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 0.088 (789 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0882 AC: 13364 AN: 151466 Hom.: 787 Cov.: 32

Gnomad AFR AF: 0.0414

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.000389

Gnomad SAS AF: 0.0337

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0882 AC: 13375 AN: 151584 Hom.: 789 Cov.: 32 AF XY: 0.0857 AC XY: 6348 AN XY: 74034

Gnomad4 AFR AF: 0.0417

Gnomad4 AMR AF: 0.0754

Gnomad4 ASJ AF: 0.0957

Gnomad4 EAS AF: 0.000390

Gnomad4 SAS AF: 0.0329

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0594 Hom.: 88

Bravo AF: 0.0872

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12487870; hg19: chr3-1551708;