rs10487129

Variant names:

• chr7-95349745-C-T
• rs10487129

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 0.0278 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
• Publications: 2 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 (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

African (AFR) AF: 0.0675 AC: 2804 AN: 41526

American (AMR) AF: 0.0173 AC: 264 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00432 AC: 15 AN: 3470

East Asian (EAS) AF: 0.0284 AC: 147 AN: 5178

South Asian (SAS) AF: 0.0222 AC: 107 AN: 4818

European-Finnish (FIN) AF: 0.0285 AC: 302 AN: 10604

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00792 AC: 539 AN: 68022

Other (OTH) AF: 0.0208 AC: 44 AN: 2112

Alfa AF: 0.0241 Hom.: 10

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
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10487129; hg19: chr7-94979057;