rs10112450

Variant names:

• chr8-103394286-T-A
• rs10112450

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 0.23 in 152,130 control chromosomes in the GnomAD database, including 4,287 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 0.23 (4287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.996
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.274 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: 0.230 AC: 35027 AN: 152012 Hom.: 4290 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.230 AC: 35048 AN: 152130 Hom.: 4287 Cov.: 32 AF XY: 0.227 AC XY: 16854 AN XY: 74376

African (AFR) AF: 0.278 AC: 11546 AN: 41488

American (AMR) AF: 0.184 AC: 2815 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1227 AN: 3466

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5182

South Asian (SAS) AF: 0.139 AC: 672 AN: 4818

European-Finnish (FIN) AF: 0.204 AC: 2163 AN: 10582

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15767 AN: 67986

Other (OTH) AF: 0.243 AC: 514 AN: 2114

Alfa AF: 0.239 Hom.: 598

Bravo AF: 0.229

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.80
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10112450; hg19: chr8-104406514;