12-97392077-G-T

Variant names:

• chr12-97392077-G-T
• rs7298683

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 0.965 in 152,198 control chromosomes in the GnomAD database, including 70,851 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 0.96 (70851 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 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: 0.965 AC: 146692 AN: 152080 Hom.: 70789 Cov.: 31

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.973

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.960

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.976

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

GnomAD4 genome AF: 0.965 AC: 146813 AN: 152198 Hom.: 70851 Cov.: 31 AF XY: 0.963 AC XY: 71656 AN XY: 74386

Gnomad4 AFR AF: 0.991

Gnomad4 AMR AF: 0.973

Gnomad4 ASJ AF: 0.965

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.960

Gnomad4 FIN AF: 0.916

Gnomad4 NFE AF: 0.951

Gnomad4 OTH AF: 0.976

Alfa AF: 0.957 Hom.: 90206

Bravo AF: 0.972

Asia WGS AF: 0.983 AC: 3420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7298683; hg19: chr12-97785855;