12-121120620-T-C

Position:

• chr12-121120620-T-C

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 0.141 in 152,046 control chromosomes in the GnomAD database, including 2,711 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 0.14 (2711 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21356 AN: 151928 Hom.: 2704 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0583

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0487

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.141 AC: 21400 AN: 152046 Hom.: 2711 Cov.: 32 AF XY: 0.142 AC XY: 10545 AN XY: 74344

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.0585

Gnomad4 ASJ AF: 0.0369

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0912

Gnomad4 NFE AF: 0.0487

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0598 Hom.: 557

Bravo AF: 0.146

Asia WGS AF: 0.210 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10849846; hg19: chr12-121558423;