rs10487129

Variant names:

• chr7-95349745-C-T
• rs10487129

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 0.0278 in 152,240 control chromosomes in the GnomAD database, including 112 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 0.028 (112 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0654 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: 0.0276 AC: 4206 AN: 152122 Hom.: 108 Cov.: 32

Gnomad AFR AF: 0.0671

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0173

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0285

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00792

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0278 AC: 4231 AN: 152240 Hom.: 112 Cov.: 32 AF XY: 0.0283 AC XY: 2104 AN XY: 74426

Gnomad4 AFR AF: 0.0675

Gnomad4 AMR AF: 0.0173

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.0284

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.0285

Gnomad4 NFE AF: 0.00792

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.0226 Hom.: 7

Bravo AF: 0.0287

Asia WGS AF: 0.0430 AC: 149 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	3.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487129; hg19: chr7-94979057;