rs10029851

chr4-108706869-A-Cchr4-108706869-A-T

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 0.176 in 152,206 control chromosomes in the GnomAD database, including 2,469 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 0.18 (2469 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26727 AN: 152088 Hom.: 2467 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.176 AC: 26756 AN: 152206 Hom.: 2469 Cov.: 33 AF XY: 0.173 AC XY: 12904 AN XY: 74426

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.0380

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.184

Alfa AF: 0.174 Hom.: 3218

Bravo AF: 0.174

Asia WGS AF: 0.114 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	6.1
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10029851; hg19: chr4-109628025;