rs12497795

Variant names:

• chr3-88928747-C-T
• rs12497795

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 0.0964 in 152,106 control chromosomes in the GnomAD database, including 1,098 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 0.096 (1098 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.243 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: 0.0964 AC: 14648 AN: 151988 Hom.: 1088 Cov.: 32

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0937

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.0952

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0964 AC: 14667 AN: 152106 Hom.: 1098 Cov.: 32 AF XY: 0.102 AC XY: 7564 AN XY: 74352

African (AFR) AF: 0.0201 AC: 834 AN: 41538

American (AMR) AF: 0.250 AC: 3811 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3468

East Asian (EAS) AF: 0.200 AC: 1035 AN: 5164

South Asian (SAS) AF: 0.129 AC: 621 AN: 4816

European-Finnish (FIN) AF: 0.0937 AC: 993 AN: 10600

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.0952 AC: 6473 AN: 67962

Other (OTH) AF: 0.108 AC: 229 AN: 2114

Alfa AF: 0.0970 Hom.: 533

Bravo AF: 0.109

Asia WGS AF: 0.165 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.32
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12497795; hg19: chr3-88977897;