rs12678919

Variant names:

• chr8-19986711-A-G
• rs12678919

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 0.0994 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.0775

Gnomad4 ASJ AF: 0.0991

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0958

Gnomad4 FIN AF: 0.0873

Gnomad4 NFE AF: 0.0984

Gnomad4 OTH AF: 0.0908

Alfa AF: 0.0992 Hom.: 1280

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12678919; hg19: chr8-19844222;