chr10-33799125-T-C

Variant names:

• chr10-33799125-T-C
• rs1412115

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 0.585 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.601

Alfa AF: 0.673 Hom.: 24902

Bravo AF: 0.570

Asia WGS AF: 0.523 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1412115; hg19: chr10-34088053;