rs12678919

Variant names:

• chr8-19986711-A-G
• rs12678919

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 0.0994 in 152,004 control chromosomes in the GnomAD database, including 756 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 0.099 (756 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 197 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 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: 0.0996 AC: 15121 AN: 151888 Hom.: 757 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.0873

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0984

Gnomad OTH AF: 0.0918

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

GnomAD4 genome AF: 0.0994 AC: 15109 AN: 152004 Hom.: 756 Cov.: 31 AF XY: 0.0985 AC XY: 7322 AN XY: 74332

African (AFR) AF: 0.111 AC: 4591 AN: 41432

American (AMR) AF: 0.0775 AC: 1184 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0991 AC: 344 AN: 3470

East Asian (EAS) AF: 0.109 AC: 558 AN: 5142

South Asian (SAS) AF: 0.0958 AC: 461 AN: 4814

European-Finnish (FIN) AF: 0.0873 AC: 924 AN: 10590

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.0984 AC: 6684 AN: 67952

Other (OTH) AF: 0.0908 AC: 192 AN: 2114

Alfa AF: 0.0985 Hom.: 3014

Bravo AF: 0.0988

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.40
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs12678919; hg19: chr8-19844222;