rs10111874

Variant names:

• chr8-109172789-A-G
• rs10111874

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 0.327 in 152,154 control chromosomes in the GnomAD database, including 8,661 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 0.33 (8661 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 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: 0.327 AC: 49657 AN: 152036 Hom.: 8655 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.327 AC: 49684 AN: 152154 Hom.: 8661 Cov.: 32 AF XY: 0.332 AC XY: 24702 AN XY: 74376

African (AFR) AF: 0.222 AC: 9210 AN: 41524

American (AMR) AF: 0.432 AC: 6601 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 687 AN: 3470

East Asian (EAS) AF: 0.470 AC: 2431 AN: 5170

South Asian (SAS) AF: 0.428 AC: 2064 AN: 4818

European-Finnish (FIN) AF: 0.392 AC: 4153 AN: 10588

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23314 AN: 67982

Other (OTH) AF: 0.313 AC: 660 AN: 2110

Alfa AF: 0.342 Hom.: 1631

Bravo AF: 0.325

Asia WGS AF: 0.472 AC: 1640 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.90
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs10111874; hg19: chr8-110185018;