10-33649088-T-C

Position:

• chr10-33649088-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 0.341 in 152,162 control chromosomes in the GnomAD database, including 11,191 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 0.34 (11191 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 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: 0.340 AC: 51741 AN: 152042 Hom.: 11164 Cov.: 33

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.341 AC: 51827 AN: 152162 Hom.: 11191 Cov.: 33 AF XY: 0.337 AC XY: 25063 AN XY: 74400

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.337

Alfa AF: 0.124 Hom.: 181

Bravo AF: 0.366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7903416; hg19: chr10-33938016;