rs12677824

Variant names:

• chr8-16930504-A-C
• rs12677824

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 0.674 in 152,116 control chromosomes in the GnomAD database, including 40,380 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 0.67 (40380 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.876 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: 0.674 AC: 102502 AN: 151998 Hom.: 40391 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.674 AC: 102490 AN: 152116 Hom.: 40380 Cov.: 33 AF XY: 0.674 AC XY: 50136 AN XY: 74354

African (AFR) AF: 0.239 AC: 9898 AN: 41472

American (AMR) AF: 0.711 AC: 10860 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2901 AN: 3470

East Asian (EAS) AF: 0.610 AC: 3143 AN: 5152

South Asian (SAS) AF: 0.800 AC: 3862 AN: 4830

European-Finnish (FIN) AF: 0.880 AC: 9316 AN: 10590

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 59965 AN: 68006

Other (OTH) AF: 0.727 AC: 1534 AN: 2110

Alfa AF: 0.637 Hom.: 2583

Bravo AF: 0.639

Asia WGS AF: 0.695 AC: 2412 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs12677824; hg19: chr8-16788013;