20-57063481-T-A

Variant names:

• chr20-57063481-T-A
• rs331615
• ENST00000748753.1:n.185+379A>T

Variant summary

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

The ENST00000748753.1(ENSG00000297537):​n.185+379A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,848 control chromosomes in the GnomAD database, including 15,294 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 0.45 (15294 hom., cov: 31)
• Consequence: ENSG00000297537 ENST00000748753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 6 publications found

Genes affected

ENSG00000297537 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748753.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297537	ENST00000748753.1		n.185+379A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67518 AN: 151730 Hom.: 15267 Cov.: 31

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.445 AC: 67579 AN: 151848 Hom.: 15294 Cov.: 31 AF XY: 0.440 AC XY: 32704 AN XY: 74244

African (AFR) AF: 0.478 AC: 19793 AN: 41402

American (AMR) AF: 0.501 AC: 7644 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1789 AN: 3470

East Asian (EAS) AF: 0.563 AC: 2891 AN: 5138

South Asian (SAS) AF: 0.277 AC: 1331 AN: 4808

European-Finnish (FIN) AF: 0.349 AC: 3690 AN: 10564

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28885 AN: 67890

Other (OTH) AF: 0.487 AC: 1029 AN: 2112

Alfa AF: 0.434 Hom.: 7898

Bravo AF: 0.468

Asia WGS AF: 0.468 AC: 1631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.45
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs331615; hg19: chr20-55638537;