rs1523921

Variant names:

• chr2-224444261-T-C
• rs1523921
• ENST00000840469.1:n.209+1208T>C

Variant summary

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

The ENST00000840469.1(ENSG00000274629):​n.209+1208T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,232 control chromosomes in the GnomAD database, including 52,696 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 0.83 (52696 hom., cov: 32)
• Consequence: ENSG00000274629 ENST00000840469.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 4 publications found

Genes affected

ENSG00000274629 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 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
ENSG00000274629	ENST00000840469.1	n.209+1208T>C		intron_variant	Intron 1 of 3
ENSG00000274629	ENST00000840470.1	n.210+1208T>C		intron_variant	Intron 1 of 2
ENSG00000274629	ENST00000840471.1	n.210-758T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126044 AN: 152114 Hom.: 52652 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.829 AC: 126149 AN: 152232 Hom.: 52696 Cov.: 32 AF XY: 0.826 AC XY: 61488 AN XY: 74436

African (AFR) AF: 0.930 AC: 38618 AN: 41538

American (AMR) AF: 0.757 AC: 11585 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2897 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3189 AN: 5176

South Asian (SAS) AF: 0.841 AC: 4058 AN: 4826

European-Finnish (FIN) AF: 0.825 AC: 8739 AN: 10598

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54477 AN: 68008

Other (OTH) AF: 0.835 AC: 1762 AN: 2110

Alfa AF: 0.803 Hom.: 36822

Bravo AF: 0.826

Asia WGS AF: 0.732 AC: 2545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.75
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1523921; hg19: chr2-225308978;