chr12-101221726-T-C

Variant names:

• chr12-101221726-T-C
• rs1631980

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 0.0707 in 152,288 control chromosomes in the GnomAD database, including 500 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 0.071 (500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0917 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: 0.0708 AC: 10773 AN: 152170 Hom.: 501 Cov.: 32

Gnomad AFR AF: 0.0343

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0720

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0690

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0936

Gnomad OTH AF: 0.0922

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

GnomAD4 genome AF: 0.0707 AC: 10772 AN: 152288 Hom.: 500 Cov.: 32 AF XY: 0.0702 AC XY: 5224 AN XY: 74454

African (AFR) AF: 0.0342 AC: 1421 AN: 41578

American (AMR) AF: 0.0717 AC: 1096 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.0693 AC: 334 AN: 4822

European-Finnish (FIN) AF: 0.0791 AC: 839 AN: 10602

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0936 AC: 6365 AN: 68016

Other (OTH) AF: 0.0912 AC: 193 AN: 2116

Alfa AF: 0.0822 Hom.: 966

Bravo AF: 0.0686

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.8
DANN	Benign	0.74
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs1631980; hg19: chr12-101615504;