rs10777288

Positions:

• chr12-91080021-G-A
• chr12-91080021-G-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;