rs2785279

chr10-33420948-T-C

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 0.318 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.318 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

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.289

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.79
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2785279; hg19: chr10-33709876;