rs1797987

Variant names:

• chr12-41129953-T-C
• rs1797987

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 0.234 in 151,812 control chromosomes in the GnomAD database, including 4,766 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 0.23 (4766 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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: 0.234 AC: 35508 AN: 151694 Hom.: 4753 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0686

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.234 AC: 35569 AN: 151812 Hom.: 4766 Cov.: 32 AF XY: 0.231 AC XY: 17158 AN XY: 74198

African (AFR) AF: 0.364 AC: 15095 AN: 41422

American (AMR) AF: 0.180 AC: 2740 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3462

East Asian (EAS) AF: 0.0686 AC: 351 AN: 5116

South Asian (SAS) AF: 0.113 AC: 543 AN: 4826

European-Finnish (FIN) AF: 0.235 AC: 2482 AN: 10572

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13271 AN: 67876

Other (OTH) AF: 0.192 AC: 403 AN: 2104

Alfa AF: 0.194 Hom.: 5207

Bravo AF: 0.234

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.3
DANN	Benign	0.83
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1797987; hg19: chr12-41523755;