chr12-91080021-G-A

Variant names:

• chr12-91080021-G-A
• rs10777288

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 0.722 in 151,862 control chromosomes in the GnomAD database, including 41,120 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 0.72 (41120 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

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 (SAS) allele frequency at 95% confidence interval = 0.821 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: 0.722 AC: 109533 AN: 151744 Hom.: 41107 Cov.: 31

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.722 AC: 109579 AN: 151862 Hom.: 41120 Cov.: 31 AF XY: 0.727 AC XY: 53961 AN XY: 74234

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.745

Alfa AF: 0.791 Hom.: 22966

Bravo AF: 0.701

Asia WGS AF: 0.734 AC: 2553 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	0.10
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10777288; hg19: chr12-91473798;