rs4452124

Variant names:

• chr2-203934974-C-T
• rs4452124
• ENST00000773540.1:n.277+1134G>A

Variant summary

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

The ENST00000773540.1(ENSG00000300710):​n.277+1134G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,174 control chromosomes in the GnomAD database, including 49,093 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 0.78 (49093 hom., cov: 33)
• Consequence: ENSG00000300710 ENST00000773540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734
• Publications: 7 publications found

Genes affected

ENSG00000300710 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927840	XR_427213.4	n.408+1134G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300710	ENST00000773540.1	n.277+1134G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118253 AN: 152056 Hom.: 49091 Cov.: 33

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.777 AC: 118273 AN: 152174 Hom.: 49093 Cov.: 33 AF XY: 0.778 AC XY: 57859 AN XY: 74412

African (AFR) AF: 0.458 AC: 18969 AN: 41454

American (AMR) AF: 0.846 AC: 12938 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2867 AN: 3470

East Asian (EAS) AF: 0.719 AC: 3721 AN: 5176

South Asian (SAS) AF: 0.870 AC: 4184 AN: 4808

European-Finnish (FIN) AF: 0.932 AC: 9896 AN: 10614

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 62984 AN: 68032

Other (OTH) AF: 0.802 AC: 1696 AN: 2114

Alfa AF: 0.876 Hom.: 207910

Bravo AF: 0.754

Asia WGS AF: 0.816 AC: 2839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.22
DANN	Benign	0.74
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs4452124; hg19: chr2-204799697;