10-33137219-T-C

Variant names:

• chr10-33137219-T-C
• rs722988

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 0.44 in 152,002 control chromosomes in the GnomAD database, including 15,481 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 0.44 (15481 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 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: 0.440 AC: 66791 AN: 151884 Hom.: 15476 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.440 AC: 66833 AN: 152002 Hom.: 15481 Cov.: 32 AF XY: 0.439 AC XY: 32588 AN XY: 74280

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.470

Alfa AF: 0.393 Hom.: 24992

Bravo AF: 0.452

Asia WGS AF: 0.626 AC: 2180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.87
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs722988; hg19: chr10-33426147;