chr12-101220625-C-T

Position:

• chr12-101220625-C-T

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 0.237 in 152,050 control chromosomes in the GnomAD database, including 4,802 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 0.24 (4802 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 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: 0.237 AC: 36024 AN: 151934 Hom.: 4802 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.237 AC: 36033 AN: 152050 Hom.: 4802 Cov.: 32 AF XY: 0.238 AC XY: 17710 AN XY: 74326

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.251

Alfa AF: 0.271 Hom.: 4654

Bravo AF: 0.231

Asia WGS AF: 0.399 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2062167; hg19: chr12-101614403;