rs1587097

Variant names:

• chr12-63136465-C-T
• rs1587097

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 0.0773 in 152,344 control chromosomes in the GnomAD database, including 608 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 0.077 (608 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 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: 0.0774 AC: 11776 AN: 152226 Hom.: 607 Cov.: 33

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.0816

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0640

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0773 AC: 11780 AN: 152344 Hom.: 608 Cov.: 33 AF XY: 0.0776 AC XY: 5777 AN XY: 74486

African (AFR) AF: 0.0201 AC: 835 AN: 41596

American (AMR) AF: 0.0815 AC: 1247 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 603 AN: 3472

East Asian (EAS) AF: 0.0349 AC: 181 AN: 5182

South Asian (SAS) AF: 0.134 AC: 647 AN: 4832

European-Finnish (FIN) AF: 0.0640 AC: 679 AN: 10606

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7170 AN: 68032

Other (OTH) AF: 0.0860 AC: 182 AN: 2116

Alfa AF: 0.0997 Hom.: 1237

Bravo AF: 0.0721

Asia WGS AF: 0.0830 AC: 288 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	5.9
DANN	Benign	0.44
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1587097; hg19: chr12-63530245;