rs733488

Variant names:

• chr10-47092629-C-G
• rs733488

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 0.295 in 152,188 control chromosomes in the GnomAD database, including 8,409 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 0.30 (8409 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.842

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 (NFE) allele frequency at 95% confidence interval = 0.408 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: 0.295 AC: 44929 AN: 152070 Hom.: 8403 Cov.: 33

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.295 AC: 44948 AN: 152188 Hom.: 8409 Cov.: 33 AF XY: 0.287 AC XY: 21376 AN XY: 74400

Gnomad4 AFR AF: 0.0985

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.340

Alfa AF: 0.346 Hom.: 1264

Bravo AF: 0.300

Asia WGS AF: 0.0870 AC: 302 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	0.53
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: rs733488; hg19: chr10-48646733;