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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;