8-90123850-T-G

Variant names:

• chr8-90123850-T-G
• rs2205108

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.545 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

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.567

Alfa AF: 0.650 Hom.: 39786

Bravo AF: 0.528

Asia WGS AF: 0.396 AC: 1377 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2205108; hg19: chr8-91136078;