8-51116860-T-G

Variant names:

• chr8-51116860-T-G
• rs10090890

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 0.254 in 152,092 control chromosomes in the GnomAD database, including 5,359 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 0.25 (5359 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.472 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: 0.254 AC: 38572 AN: 151972 Hom.: 5346 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.254 AC: 38618 AN: 152092 Hom.: 5359 Cov.: 33 AF XY: 0.256 AC XY: 18995 AN XY: 74342

African (AFR) AF: 0.158 AC: 6565 AN: 41480

American (AMR) AF: 0.313 AC: 4792 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1164 AN: 3470

East Asian (EAS) AF: 0.241 AC: 1245 AN: 5172

South Asian (SAS) AF: 0.489 AC: 2355 AN: 4820

European-Finnish (FIN) AF: 0.222 AC: 2352 AN: 10578

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19094 AN: 67970

Other (OTH) AF: 0.280 AC: 592 AN: 2114

Alfa AF: 0.269 Hom.: 8861

Bravo AF: 0.256

Asia WGS AF: 0.369 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.45
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs10090890; hg19: chr8-52029420;