8-109207506-T-C

Variant names:

• chr8-109207506-T-C
• rs10087444

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 0.638 in 151,976 control chromosomes in the GnomAD database, including 32,392 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 0.64 (32392 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 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: 0.637 AC: 96800 AN: 151858 Hom.: 32339 Cov.: 31

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.638 AC: 96915 AN: 151976 Hom.: 32392 Cov.: 31 AF XY: 0.637 AC XY: 47274 AN XY: 74258

African (AFR) AF: 0.847 AC: 35114 AN: 41478

American (AMR) AF: 0.656 AC: 10010 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1399 AN: 3468

East Asian (EAS) AF: 0.528 AC: 2717 AN: 5148

South Asian (SAS) AF: 0.667 AC: 3213 AN: 4816

European-Finnish (FIN) AF: 0.521 AC: 5501 AN: 10562

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36855 AN: 67940

Other (OTH) AF: 0.627 AC: 1322 AN: 2110

Alfa AF: 0.582 Hom.: 48700

Bravo AF: 0.653

Asia WGS AF: 0.658 AC: 2291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.55
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs10087444; hg19: chr8-110219735; COSMIC: COSV65222127;