rs2633323

Variant names:

• chr10-73935068-G-A
• rs2633323

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 0.449 in 152,010 control chromosomes in the GnomAD database, including 16,566 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 0.45 (16566 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 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: 0.449 AC: 68247 AN: 151892 Hom.: 16565 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.449 AC: 68255 AN: 152010 Hom.: 16566 Cov.: 31 AF XY: 0.443 AC XY: 32909 AN XY: 74280

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.518

Alfa AF: 0.484 Hom.: 3403

Bravo AF: 0.443

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2633323; hg19: chr10-75694826;