12-97282457-G-A

Position:

• chr12-97282457-G-A

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 0.078 in 152,168 control chromosomes in the GnomAD database, including 656 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 0.078 (656 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 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: 0.0780 AC: 11853 AN: 152050 Hom.: 653 Cov.: 31

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0805

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0858

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

GnomAD4 genome AF: 0.0780 AC: 11864 AN: 152168 Hom.: 656 Cov.: 31 AF XY: 0.0776 AC XY: 5772 AN XY: 74384

Gnomad4 AFR AF: 0.0187

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.0878

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0812

Gnomad4 FIN AF: 0.0718

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0844

Alfa AF: 0.0929 Hom.: 322

Bravo AF: 0.0807

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1558726; hg19: chr12-97676235;