chr10-33649088-T-C

Variant names:

• chr10-33649088-T-C
• rs7903416

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;