rs4397388

Positions:

• chr8-57741648-A-G

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, non coding transcript 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: ENST00000520426.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000520426.1	n.273+44910T>C		intron_variant, non_coding_transcript_variant		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;