12-91102061-T-C

Variant names:

• chr12-91102061-T-C
• rs7976738

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.820 AC: 33995 AN: 41476

American (AMR) AF: 0.874 AC: 13302 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3060 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5158 AN: 5164

South Asian (SAS) AF: 0.949 AC: 4585 AN: 4830

European-Finnish (FIN) AF: 0.911 AC: 9653 AN: 10598

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 57999 AN: 67894

Other (OTH) AF: 0.856 AC: 1807 AN: 2110

Alfa AF: 0.853 Hom.: 67484

Bravo AF: 0.855

Asia WGS AF: 0.961 AC: 3342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.35
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs7976738; hg19: chr12-91495838;