rs4397388

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000253322 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.604 AC: 25003 AN: 41424

American (AMR) AF: 0.522 AC: 7959 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1901 AN: 3466

East Asian (EAS) AF: 0.338 AC: 1746 AN: 5162

South Asian (SAS) AF: 0.300 AC: 1443 AN: 4814

European-Finnish (FIN) AF: 0.345 AC: 3647 AN: 10558

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.423 AC: 28748 AN: 67942

Other (OTH) AF: 0.482 AC: 1015 AN: 2106

Alfa AF: 0.467 Hom.: 2533

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
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs4397388; hg19: chr8-58654207;