chr8-127519892-T-C

Variant names:

• chr8-127519892-T-C
• rs10090154

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 0.877 in 152,086 control chromosomes in the GnomAD database, including 58,598 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 0.88 (58598 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.404
• Publications: 81 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.907 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: 0.877 AC: 133270 AN: 151968 Hom.: 58560 Cov.: 31

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.877 AC: 133363 AN: 152086 Hom.: 58598 Cov.: 31 AF XY: 0.876 AC XY: 65135 AN XY: 74338

African (AFR) AF: 0.828 AC: 34331 AN: 41480

American (AMR) AF: 0.919 AC: 14056 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.938 AC: 3255 AN: 3470

East Asian (EAS) AF: 0.857 AC: 4443 AN: 5182

South Asian (SAS) AF: 0.867 AC: 4181 AN: 4820

European-Finnish (FIN) AF: 0.838 AC: 8808 AN: 10514

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.901 AC: 61291 AN: 68010

Other (OTH) AF: 0.895 AC: 1894 AN: 2116

Alfa AF: 0.892 Hom.: 119937

Bravo AF: 0.879

Asia WGS AF: 0.818 AC: 2842 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	7.0
DANN	Benign	0.96
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10090154; hg19: chr8-128532137;