chr12-91075350-G-A

Variant names:

• chr12-91075350-G-A
• rs10777286

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 0.444 in 151,814 control chromosomes in the GnomAD database, including 15,355 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 0.44 (15355 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67328 AN: 151696 Hom.: 15350 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.444 AC: 67376 AN: 151814 Hom.: 15355 Cov.: 31 AF XY: 0.451 AC XY: 33441 AN XY: 74180

African (AFR) AF: 0.495 AC: 20473 AN: 41380

American (AMR) AF: 0.432 AC: 6581 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1483 AN: 3468

East Asian (EAS) AF: 0.712 AC: 3650 AN: 5126

South Asian (SAS) AF: 0.519 AC: 2492 AN: 4806

European-Finnish (FIN) AF: 0.478 AC: 5035 AN: 10528

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.386 AC: 26239 AN: 67946

Other (OTH) AF: 0.457 AC: 965 AN: 2112

Alfa AF: 0.408 Hom.: 18599

Bravo AF: 0.439

Asia WGS AF: 0.606 AC: 2106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.62
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10777286; hg19: chr12-91469127;