rs4397388

Variant names:

• chr8-57741648-A-G
• rs4397388
• ENST00000520426.1:n.273+44910T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000520426.1(ENSG00000253322):​n.273+44910T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,928 control chromosomes in the GnomAD database, including 17,830 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 0.47 (17830 hom., cov: 31)
• Consequence: ENSG00000253322 ENST00000520426.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

Genes affected

ENSG00000253322 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 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
ENSG00000253322	ENST00000520426.1	n.273+44910T>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71862 AN: 151810 Hom.: 17797 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.474 AC: 71944 AN: 151928 Hom.: 17830 Cov.: 31 AF XY: 0.466 AC XY: 34612 AN XY: 74244

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.482

Alfa AF: 0.462 Hom.: 2393

Bravo AF: 0.493

Asia WGS AF: 0.387 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4397388; hg19: chr8-58654207;