rs10777286

Positions:

• chr12-91075350-G-A
• chr12-91075350-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 0.444 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

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 (EAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.457

Alfa AF: 0.399 Hom.: 11863

Bravo AF: 0.439

Asia WGS AF: 0.606 AC: 2106 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	1.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10777286; hg19: chr12-91469127;