8-90123850-T-G

Variant names:

• chr8-90123850-T-G
• rs2205108

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 0.545 in 151,974 control chromosomes in the GnomAD database, including 24,199 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 0.54 (24199 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 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: 0.545 AC: 82774 AN: 151856 Hom.: 24205 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.545 AC: 82785 AN: 151974 Hom.: 24199 Cov.: 32 AF XY: 0.538 AC XY: 39988 AN XY: 74286

African (AFR) AF: 0.353 AC: 14648 AN: 41488

American (AMR) AF: 0.490 AC: 7471 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2437 AN: 3472

East Asian (EAS) AF: 0.309 AC: 1595 AN: 5170

South Asian (SAS) AF: 0.531 AC: 2557 AN: 4814

European-Finnish (FIN) AF: 0.595 AC: 6267 AN: 10540

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45752 AN: 67924

Other (OTH) AF: 0.567 AC: 1194 AN: 2106

Alfa AF: 0.637 Hom.: 48854

Bravo AF: 0.528

Asia WGS AF: 0.396 AC: 1377 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	14
DANN	Benign	0.76
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs2205108; hg19: chr8-91136078;