12-105983670-T-C

Variant names:

• chr12-105983670-T-C
• rs1862032

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 0.64 in 152,036 control chromosomes in the GnomAD database, including 32,235 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 0.64 (32235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 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: 0.641 AC: 97338 AN: 151918 Hom.: 32235 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.640 AC: 97358 AN: 152036 Hom.: 32235 Cov.: 32 AF XY: 0.642 AC XY: 47712 AN XY: 74334

African (AFR) AF: 0.464 AC: 19249 AN: 41452

American (AMR) AF: 0.636 AC: 9697 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2464 AN: 3470

East Asian (EAS) AF: 0.692 AC: 3574 AN: 5166

South Asian (SAS) AF: 0.529 AC: 2545 AN: 4810

European-Finnish (FIN) AF: 0.789 AC: 8356 AN: 10584

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49161 AN: 67980

Other (OTH) AF: 0.670 AC: 1414 AN: 2110

Alfa AF: 0.670 Hom.: 5884

Bravo AF: 0.628

Asia WGS AF: 0.595 AC: 2069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.7
DANN	Benign	0.76
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs1862032; hg19: chr12-106377448;