chr8-142684467-G-A

Variant names:

• chr8-142684467-G-A
• rs12155758

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 0.23 in 152,168 control chromosomes in the GnomAD database, including 4,590 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 0.23 (4590 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.317 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: 0.230 AC: 34941 AN: 152050 Hom.: 4579 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.230 AC: 34963 AN: 152168 Hom.: 4590 Cov.: 33 AF XY: 0.233 AC XY: 17310 AN XY: 74398

African (AFR) AF: 0.119 AC: 4930 AN: 41536

American (AMR) AF: 0.324 AC: 4955 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 886 AN: 3470

East Asian (EAS) AF: 0.146 AC: 755 AN: 5160

South Asian (SAS) AF: 0.237 AC: 1142 AN: 4824

European-Finnish (FIN) AF: 0.319 AC: 3377 AN: 10592

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18162 AN: 67978

Other (OTH) AF: 0.229 AC: 484 AN: 2112

Alfa AF: 0.246 Hom.: 10879

Bravo AF: 0.222

Asia WGS AF: 0.184 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.56
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12155758; hg19: chr8-143765885;