rs2633317

Positions:

• chr10-73930510-A-G

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 0.506 in 152,106 control chromosomes in the GnomAD database, including 20,249 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 0.51 (20249 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76968 AN: 151986 Hom.: 20245 Cov.: 33

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.506 AC: 76998 AN: 152106 Hom.: 20249 Cov.: 33 AF XY: 0.498 AC XY: 37039 AN XY: 74348

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.575

Alfa AF: 0.534 Hom.: 2806

Bravo AF: 0.506

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.96
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2633317; hg19: chr10-75690268;