rs12678919

Positions:

• chr8-19986711-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;