rs12495098

Variant names:

• chr3-46301011-T-G
• rs12495098

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 0.101 in 152,212 control chromosomes in the GnomAD database, including 884 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 0.10 (884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 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: 0.101 AC: 15404 AN: 152096 Hom.: 881 Cov.: 32

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.0872

Gnomad FIN AF: 0.0611

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0865

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.101 AC: 15421 AN: 152212 Hom.: 884 Cov.: 32 AF XY: 0.102 AC XY: 7617 AN XY: 74426

African (AFR) AF: 0.100 AC: 4159 AN: 41528

American (AMR) AF: 0.162 AC: 2472 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1064 AN: 5170

South Asian (SAS) AF: 0.0869 AC: 419 AN: 4824

European-Finnish (FIN) AF: 0.0611 AC: 649 AN: 10616

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0865 AC: 5882 AN: 68010

Other (OTH) AF: 0.113 AC: 239 AN: 2114

Alfa AF: 0.102 Hom.: 130

Bravo AF: 0.111

Asia WGS AF: 0.159 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs12495098; hg19: chr3-46342502;