12-119886217-T-C

Variant names:

• chr12-119886217-T-C
• rs7960673

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 0.714 in 152,068 control chromosomes in the GnomAD database, including 39,095 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 0.71 (39095 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.888 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: 0.714 AC: 108447 AN: 151950 Hom.: 39052 Cov.: 33

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.714 AC: 108557 AN: 152068 Hom.: 39095 Cov.: 33 AF XY: 0.719 AC XY: 53430 AN XY: 74344

African (AFR) AF: 0.650 AC: 26957 AN: 41452

American (AMR) AF: 0.766 AC: 11694 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2551 AN: 3468

East Asian (EAS) AF: 0.910 AC: 4702 AN: 5168

South Asian (SAS) AF: 0.664 AC: 3204 AN: 4822

European-Finnish (FIN) AF: 0.782 AC: 8276 AN: 10586

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48903 AN: 67988

Other (OTH) AF: 0.719 AC: 1517 AN: 2110

Alfa AF: 0.717 Hom.: 58460

Bravo AF: 0.713

Asia WGS AF: 0.774 AC: 2689 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	2.4
DANN	Benign	0.62
PhyloP100		0.096

Splicing

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

Other links and lift over

dbSNP: rs7960673; hg19: chr12-120324021;