chr10-9106732-C-T

Variant names:

• chr10-9106732-C-T
• rs10490947

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 0.0266 in 152,036 control chromosomes in the GnomAD database, including 139 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 0.027 (139 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.996
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.098 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: 0.0265 AC: 4032 AN: 151918 Hom.: 134 Cov.: 31

Gnomad AFR AF: 0.00600

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.00271

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0266 AC: 4050 AN: 152036 Hom.: 139 Cov.: 31 AF XY: 0.0284 AC XY: 2112 AN XY: 74292

African (AFR) AF: 0.00598 AC: 248 AN: 41460

American (AMR) AF: 0.102 AC: 1561 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3468

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5158

South Asian (SAS) AF: 0.0172 AC: 83 AN: 4820

European-Finnish (FIN) AF: 0.0268 AC: 283 AN: 10552

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0263 AC: 1788 AN: 67994

Other (OTH) AF: 0.0246 AC: 52 AN: 2112

Alfa AF: 0.0263 Hom.: 12

Bravo AF: 0.0316

Asia WGS AF: 0.0120 AC: 41 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	8.7
DANN	Benign	0.68
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10490947; hg19: chr10-9148695;