10-33799125-T-C

Variant names:

• chr10-33799125-T-C
• rs1412115

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 0.585 in 151,962 control chromosomes in the GnomAD database, including 28,299 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 0.58 (28299 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88803 AN: 151844 Hom.: 28286 Cov.: 30

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.585 AC: 88844 AN: 151962 Hom.: 28299 Cov.: 30 AF XY: 0.586 AC XY: 43537 AN XY: 74264

African (AFR) AF: 0.312 AC: 12933 AN: 41450

American (AMR) AF: 0.691 AC: 10551 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2491 AN: 3466

East Asian (EAS) AF: 0.520 AC: 2670 AN: 5132

South Asian (SAS) AF: 0.486 AC: 2330 AN: 4796

European-Finnish (FIN) AF: 0.747 AC: 7900 AN: 10578

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47902 AN: 67956

Other (OTH) AF: 0.601 AC: 1264 AN: 2104

Alfa AF: 0.636 Hom.: 49441

Bravo AF: 0.570

Asia WGS AF: 0.523 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.81
DANN	Benign	0.44
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1412115; hg19: chr10-34088053;