rs7100129

Variant names:

• chr10-90865388-C-T
• rs7100129

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.159 in 151,934 control chromosomes in the GnomAD database, including 2,899 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 0.16 (2899 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 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: 0.158 AC: 24060 AN: 151816 Hom.: 2891 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0902

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.159 AC: 24092 AN: 151934 Hom.: 2899 Cov.: 32 AF XY: 0.162 AC XY: 12038 AN XY: 74280

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.0903

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.0902

Gnomad4 NFE AF: 0.0633

Gnomad4 OTH AF: 0.151

Alfa AF: 0.117 Hom.: 389

Bravo AF: 0.171

Asia WGS AF: 0.222 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7100129; hg19: chr10-92625145;