chr10-34906478-G-A

Variant names:

• chr10-34906478-G-A
• rs2492448

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 0.31 in 152,062 control chromosomes in the GnomAD database, including 7,439 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 0.31 (7439 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 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: 0.310 AC: 47072 AN: 151944 Hom.: 7426 Cov.: 33

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.310 AC: 47134 AN: 152062 Hom.: 7439 Cov.: 33 AF XY: 0.308 AC XY: 22863 AN XY: 74332

African (AFR) AF: 0.360 AC: 14910 AN: 41474

American (AMR) AF: 0.316 AC: 4821 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1140 AN: 3464

East Asian (EAS) AF: 0.273 AC: 1414 AN: 5174

South Asian (SAS) AF: 0.348 AC: 1677 AN: 4814

European-Finnish (FIN) AF: 0.264 AC: 2792 AN: 10576

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.287 AC: 19507 AN: 67976

Other (OTH) AF: 0.289 AC: 612 AN: 2116

Alfa AF: 0.296 Hom.: 29336

Bravo AF: 0.318

Asia WGS AF: 0.342 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.25
DANN	Benign	0.76
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs2492448; hg19: chr10-35195406;