chr10-89204857-T-G

Variant names:

• chr10-89204857-T-G
• rs11203032

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 0.135 in 152,234 control chromosomes in the GnomAD database, including 2,940 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 0.13 (2940 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.848
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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: 0.135 AC: 20516 AN: 152116 Hom.: 2929 Cov.: 33

Gnomad AFR AF: 0.0247

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.135 AC: 20547 AN: 152234 Hom.: 2940 Cov.: 33 AF XY: 0.147 AC XY: 10926 AN XY: 74412

African (AFR) AF: 0.0247 AC: 1028 AN: 41558

American (AMR) AF: 0.215 AC: 3292 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3472

East Asian (EAS) AF: 0.758 AC: 3921 AN: 5170

South Asian (SAS) AF: 0.323 AC: 1557 AN: 4826

European-Finnish (FIN) AF: 0.236 AC: 2500 AN: 10590

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7235 AN: 68010

Other (OTH) AF: 0.138 AC: 292 AN: 2112

Alfa AF: 0.119 Hom.: 3140

Bravo AF: 0.131

Asia WGS AF: 0.457 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.8
DANN	Benign	0.78
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs11203032; hg19: chr10-90964614;