12-105934476-T-C

Variant names:

• chr12-105934476-T-C
• rs2111980

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.485 in 151,970 control chromosomes in the GnomAD database, including 18,670 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 0.48 (18670 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.558 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: 0.485 AC: 73671 AN: 151852 Hom.: 18670 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.485 AC: 73681 AN: 151970 Hom.: 18670 Cov.: 31 AF XY: 0.488 AC XY: 36211 AN XY: 74264

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.461

Alfa AF: 0.539 Hom.: 29190

Bravo AF: 0.466

Asia WGS AF: 0.445 AC: 1551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	14
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2111980; hg19: chr12-106328254;