chr8-42695355-C-T

Variant names:

• chr8-42695355-C-T
• rs6474412

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 0.649 in 152,006 control chromosomes in the GnomAD database, including 34,872 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 0.65 (34872 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 63 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98646 AN: 151888 Hom.: 34860 Cov.: 31

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.649 AC: 98686 AN: 152006 Hom.: 34872 Cov.: 31 AF XY: 0.654 AC XY: 48576 AN XY: 74306

African (AFR) AF: 0.347 AC: 14393 AN: 41426

American (AMR) AF: 0.717 AC: 10937 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2449 AN: 3472

East Asian (EAS) AF: 0.806 AC: 4172 AN: 5174

South Asian (SAS) AF: 0.712 AC: 3430 AN: 4820

European-Finnish (FIN) AF: 0.760 AC: 8033 AN: 10568

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.778 AC: 52877 AN: 67966

Other (OTH) AF: 0.682 AC: 1442 AN: 2114

Alfa AF: 0.732 Hom.: 102097

Bravo AF: 0.631

Asia WGS AF: 0.711 AC: 2470 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	0.049
DANN	Benign	0.63
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6474412; hg19: chr8-42550498;