rs2413583

Variant names:

• chr22-39263768-C-T
• rs2413583
• ENST00000641859.1:n.110-12808C>T

Variant summary

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

The ENST00000641859.1(ENSG00000284633):​n.110-12808C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,142 control chromosomes in the GnomAD database, including 3,144 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 0.19 (3144 hom., cov: 32)
• Consequence: ENSG00000284633 ENST00000641859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24
• Publications: 69 publications found

Genes affected

ENSG00000284633 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 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
ENSG00000284633	ENST00000641859.1	n.110-12808C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28771 AN: 152024 Hom.: 3133 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0580

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.189 AC: 28818 AN: 152142 Hom.: 3144 Cov.: 32 AF XY: 0.183 AC XY: 13634 AN XY: 74358

African (AFR) AF: 0.292 AC: 12127 AN: 41462

American (AMR) AF: 0.123 AC: 1881 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3470

East Asian (EAS) AF: 0.0583 AC: 302 AN: 5182

South Asian (SAS) AF: 0.157 AC: 757 AN: 4822

European-Finnish (FIN) AF: 0.107 AC: 1131 AN: 10602

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11283 AN: 67990

Other (OTH) AF: 0.185 AC: 389 AN: 2108

Alfa AF: 0.172 Hom.: 11265

Bravo AF: 0.195

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.17
DANN	Benign	0.41
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs2413583; hg19: chr22-39659773;