rs2633323

Positions:

• chr10-73935068-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;