chr10-128450662-T-G

Variant names:

• chr10-128450662-T-G
• rs9804317

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 0.138 in 152,158 control chromosomes in the GnomAD database, including 1,913 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 0.14 (1913 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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: 0.138 AC: 20989 AN: 152040 Hom.: 1910 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.0673

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.0827

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.138 AC: 20998 AN: 152158 Hom.: 1913 Cov.: 33 AF XY: 0.143 AC XY: 10615 AN XY: 74404

African (AFR) AF: 0.203 AC: 8413 AN: 41494

American (AMR) AF: 0.144 AC: 2207 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2067 AN: 5162

South Asian (SAS) AF: 0.248 AC: 1196 AN: 4818

European-Finnish (FIN) AF: 0.0673 AC: 713 AN: 10600

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.0827 AC: 5627 AN: 68004

Other (OTH) AF: 0.132 AC: 278 AN: 2110

Alfa AF: 0.105 Hom.: 4878

Bravo AF: 0.148

Asia WGS AF: 0.313 AC: 1088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.32
DANN	Benign	0.61
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9804317; hg19: chr10-130248926;