chr12-97637847-C-T

Position:

• chr12-97637847-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 0.0524 in 152,184 control chromosomes in the GnomAD database, including 316 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 0.052 (316 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

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 = 0.0902 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: 0.0525 AC: 7978 AN: 152066 Hom.: 317 Cov.: 33

Gnomad AFR AF: 0.0266

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0690

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.0974

Gnomad SAS AF: 0.0696

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0524 AC: 7975 AN: 152184 Hom.: 316 Cov.: 33 AF XY: 0.0577 AC XY: 4295 AN XY: 74402

Gnomad4 AFR AF: 0.0265

Gnomad4 AMR AF: 0.0689

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.0973

Gnomad4 SAS AF: 0.0697

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.0475

Gnomad4 OTH AF: 0.0502

Alfa AF: 0.0566 Hom.: 88

Bravo AF: 0.0450

Asia WGS AF: 0.100 AC: 345 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	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1376345; hg19: chr12-98031625;