rs10029851

Variant names:

• chr4-108706869-A-C
• rs10029851

Your query was ambiguous. Multiple possible variants found:

• chr4-108706869-A-C
• chr4-108706869-A-T

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 0.176 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.195 AC: 8103 AN: 41526

American (AMR) AF: 0.139 AC: 2130 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3468

East Asian (EAS) AF: 0.0380 AC: 196 AN: 5160

South Asian (SAS) AF: 0.167 AC: 805 AN: 4830

European-Finnish (FIN) AF: 0.151 AC: 1599 AN: 10608

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12569 AN: 68002

Other (OTH) AF: 0.184 AC: 390 AN: 2116

Alfa AF: 0.176 Hom.: 4629

Bravo AF: 0.174

Asia WGS AF: 0.114 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.1
DANN	Benign	0.79
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs10029851; hg19: chr4-109628025;