8-89198871-A-G

Variant names:

• chr8-89198871-A-G
• rs2046315

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 0.72 in 152,016 control chromosomes in the GnomAD database, including 42,391 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 0.72 (42391 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 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: 0.720 AC: 109362 AN: 151898 Hom.: 42383 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.720 AC: 109402 AN: 152016 Hom.: 42391 Cov.: 32 AF XY: 0.721 AC XY: 53599 AN XY: 74296

African (AFR) AF: 0.407 AC: 16893 AN: 41464

American (AMR) AF: 0.754 AC: 11481 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2888 AN: 3470

East Asian (EAS) AF: 0.673 AC: 3472 AN: 5158

South Asian (SAS) AF: 0.790 AC: 3808 AN: 4822

European-Finnish (FIN) AF: 0.829 AC: 8776 AN: 10590

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59433 AN: 67976

Other (OTH) AF: 0.747 AC: 1574 AN: 2108

Alfa AF: 0.814 Hom.: 164590

Bravo AF: 0.699

Asia WGS AF: 0.691 AC: 2408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.57
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs2046315; hg19: chr8-90211100;