rs776893

Variant names:

• chr12-41110542-A-G
• rs776893

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 0.609 in 151,924 control chromosomes in the GnomAD database, including 29,700 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 0.61 (29700 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 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: 0.609 AC: 92470 AN: 151806 Hom.: 29668 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.609 AC: 92550 AN: 151924 Hom.: 29700 Cov.: 32 AF XY: 0.608 AC XY: 45108 AN XY: 74240

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.567

Alfa AF: 0.535 Hom.: 43939

Bravo AF: 0.614

Asia WGS AF: 0.471 AC: 1637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.80
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs776893; hg19: chr12-41504344;