rs1587097

chr12-63136465-C-T

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 0.0773 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

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 (SAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0201

Gnomad4 AMR AF: 0.0815

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.0349

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.0640

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0860

Alfa AF: 0.100 Hom.: 1077

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1587097; hg19: chr12-63530245;