12-91102061-T-C

Variant names:

• chr12-91102061-T-C
• rs7976738

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 0.858 in 151,964 control chromosomes in the GnomAD database, including 56,146 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 0.86 (56146 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.859 AC: 130368 AN: 151846 Hom.: 56116 Cov.: 30

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.858 AC: 130453 AN: 151964 Hom.: 56146 Cov.: 30 AF XY: 0.862 AC XY: 63986 AN XY: 74270

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.949

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.854

Gnomad4 OTH AF: 0.856

Alfa AF: 0.852 Hom.: 50686

Bravo AF: 0.855

Asia WGS AF: 0.961 AC: 3342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7976738; hg19: chr12-91495838;