chr10-30396607-T-A

Variant names:

• chr10-30396607-T-A
• rs34951790

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 0.125 in 152,268 control chromosomes in the GnomAD database, including 1,503 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 0.12 (1503 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19010 AN: 152150 Hom.: 1504 Cov.: 32

Gnomad AFR AF: 0.0422

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0650

Gnomad SAS AF: 0.0683

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.125 AC: 19015 AN: 152268 Hom.: 1503 Cov.: 32 AF XY: 0.125 AC XY: 9312 AN XY: 74436

African (AFR) AF: 0.0422 AC: 1755 AN: 41570

American (AMR) AF: 0.199 AC: 3048 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3470

East Asian (EAS) AF: 0.0652 AC: 338 AN: 5188

South Asian (SAS) AF: 0.0685 AC: 331 AN: 4830

European-Finnish (FIN) AF: 0.164 AC: 1736 AN: 10592

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11027 AN: 68008

Other (OTH) AF: 0.138 AC: 292 AN: 2112

Alfa AF: 0.157 Hom.: 249

Bravo AF: 0.125

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.6
DANN	Benign	0.90
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs34951790; hg19: chr10-30685536;