12-121123168-T-C

Position:

• chr12-121123168-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 0.108 in 152,128 control chromosomes in the GnomAD database, including 1,508 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 0.11 (1508 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16379 AN: 152010 Hom.: 1504 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0458

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0792

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.108 AC: 16404 AN: 152128 Hom.: 1508 Cov.: 31 AF XY: 0.109 AC XY: 8123 AN XY: 74366

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.0460

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0792

Gnomad4 NFE AF: 0.0433

Gnomad4 OTH AF: 0.0771

Alfa AF: 0.0808 Hom.: 121

Bravo AF: 0.110

Asia WGS AF: 0.200 AC: 693 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	2.4
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11065441; hg19: chr12-121560971;