chr12-17209882-G-C

Variant names:

• chr12-17209882-G-C
• rs1513049

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 0.901 in 152,282 control chromosomes in the GnomAD database, including 62,583 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 0.90 (62583 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.974 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: 0.901 AC: 137159 AN: 152164 Hom.: 62548 Cov.: 33

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.901 AC: 137248 AN: 152282 Hom.: 62583 Cov.: 33 AF XY: 0.900 AC XY: 67026 AN XY: 74466

African (AFR) AF: 0.761 AC: 31580 AN: 41516

American (AMR) AF: 0.888 AC: 13579 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.992 AC: 3443 AN: 3472

East Asian (EAS) AF: 0.797 AC: 4126 AN: 5178

South Asian (SAS) AF: 0.916 AC: 4425 AN: 4830

European-Finnish (FIN) AF: 0.963 AC: 10229 AN: 10624

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.981 AC: 66728 AN: 68042

Other (OTH) AF: 0.923 AC: 1954 AN: 2116

Alfa AF: 0.948 Hom.: 3347

Bravo AF: 0.890

Asia WGS AF: 0.858 AC: 2985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.037
DANN	Benign	0.54
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1513049; hg19: chr12-17362816;