rs2785279

Variant names:

• chr10-33420948-T-C
• rs2785279

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 0.318 in 152,040 control chromosomes in the GnomAD database, including 12,191 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 0.32 (12191 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.645
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 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: 0.318 AC: 48300 AN: 151922 Hom.: 12163 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.318 AC: 48378 AN: 152040 Hom.: 12191 Cov.: 32 AF XY: 0.311 AC XY: 23116 AN XY: 74320

African (AFR) AF: 0.710 AC: 29434 AN: 41438

American (AMR) AF: 0.206 AC: 3148 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 692 AN: 3472

East Asian (EAS) AF: 0.167 AC: 859 AN: 5156

South Asian (SAS) AF: 0.149 AC: 719 AN: 4812

European-Finnish (FIN) AF: 0.137 AC: 1454 AN: 10582

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11187 AN: 67980

Other (OTH) AF: 0.289 AC: 611 AN: 2112

Alfa AF: 0.256 Hom.: 1185

Bravo AF: 0.345

Asia WGS AF: 0.185 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.79
DANN	Benign	0.34
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2785279; hg19: chr10-33709876;