rs776893

Variant names:

• chr12-41110542-A-G
• rs776893

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 0.609 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.826 AC: 34241 AN: 41476

American (AMR) AF: 0.508 AC: 7735 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1915 AN: 3468

East Asian (EAS) AF: 0.421 AC: 2166 AN: 5142

South Asian (SAS) AF: 0.496 AC: 2385 AN: 4812

European-Finnish (FIN) AF: 0.578 AC: 6095 AN: 10546

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36119 AN: 67952

Other (OTH) AF: 0.567 AC: 1197 AN: 2110

Alfa AF: 0.552 Hom.: 75241

Bravo AF: 0.614

Asia WGS AF: 0.471 AC: 1637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.80
DANN	Benign	0.39
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs776893; hg19: chr12-41504344;