8-42688874-A-G

Variant names:

• chr8-42688874-A-G
• rs13273442

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 0.665 in 152,042 control chromosomes in the GnomAD database, including 35,789 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 0.66 (35789 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 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: 0.665 AC: 100998 AN: 151922 Hom.: 35773 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.665 AC: 101046 AN: 152042 Hom.: 35789 Cov.: 31 AF XY: 0.668 AC XY: 49662 AN XY: 74308

African (AFR) AF: 0.400 AC: 16569 AN: 41442

American (AMR) AF: 0.724 AC: 11062 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2462 AN: 3468

East Asian (EAS) AF: 0.806 AC: 4166 AN: 5168

South Asian (SAS) AF: 0.712 AC: 3429 AN: 4816

European-Finnish (FIN) AF: 0.761 AC: 8050 AN: 10584

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52904 AN: 67976

Other (OTH) AF: 0.689 AC: 1455 AN: 2112

Alfa AF: 0.738 Hom.: 133368

Bravo AF: 0.650

Asia WGS AF: 0.713 AC: 2478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.34
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs13273442; hg19: chr8-42544017;