rs2633580

Variant names:

• chr3-112500906-C-G
• rs2633580
• ENST00000793585.1:n.393-17102C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000793585.1(ENSG00000303317):​n.393-17102C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 151,918 control chromosomes in the GnomAD database, including 8,008 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 0.24 (8008 hom., cov: 31)
• Consequence: ENSG00000303317 ENST00000793585.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657
• Publications: 4 publications found

Genes affected

ENSG00000303317 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 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
ENSG00000303317	ENST00000793585.1	n.393-17102C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36588 AN: 151800 Hom.: 7970 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.0666

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.241 AC: 36675 AN: 151918 Hom.: 8008 Cov.: 31 AF XY: 0.240 AC XY: 17806 AN XY: 74244

African (AFR) AF: 0.574 AC: 23744 AN: 41390

American (AMR) AF: 0.251 AC: 3822 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1259 AN: 5166

South Asian (SAS) AF: 0.179 AC: 860 AN: 4814

European-Finnish (FIN) AF: 0.0666 AC: 705 AN: 10578

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0791 AC: 5373 AN: 67940

Other (OTH) AF: 0.219 AC: 462 AN: 2110

Alfa AF: 0.174 Hom.: 602

Bravo AF: 0.275

Asia WGS AF: 0.216 AC: 750 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.43
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs2633580; hg19: chr3-112219753;