ENST00000523784.2:n.504+3658C>T

Variant names:

• chr8-100459937-C-T
• rs2022922
• ENST00000523784.2:n.504+3658C>T

Variant summary

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

The ENST00000523784.2(ENSG00000253666):​n.504+3658C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 151,978 control chromosomes in the GnomAD database, including 36,092 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 0.67 (36092 hom., cov: 30)
• Consequence: ENSG00000253666 ENST00000523784.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88
• Publications: 3 publications found

Genes affected

ENSG00000253666 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.784 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
ENSG00000253666	ENST00000523784.2	n.504+3658C>T		intron_variant	Intron 4 of 5	3
ENSG00000253824	ENST00000664475.1	n.119+4558G>A		intron_variant	Intron 1 of 1
ENSG00000253666	ENST00000716448.1	n.736-1719C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102039 AN: 151860 Hom.: 36076 Cov.: 30

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.672 AC: 102092 AN: 151978 Hom.: 36092 Cov.: 30 AF XY: 0.670 AC XY: 49750 AN XY: 74282

African (AFR) AF: 0.469 AC: 19391 AN: 41384

American (AMR) AF: 0.704 AC: 10750 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2581 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2496 AN: 5154

South Asian (SAS) AF: 0.468 AC: 2252 AN: 4810

European-Finnish (FIN) AF: 0.824 AC: 8717 AN: 10574

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53715 AN: 67996

Other (OTH) AF: 0.651 AC: 1372 AN: 2106

Alfa AF: 0.734 Hom.: 16240

Bravo AF: 0.659

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	0.27
DANN	Benign	0.93
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs2022922; hg19: chr8-101472165;