20-21904055-G-A

Variant names:

• chr20-21904055-G-A
• rs6137473
• ENST00000813851.1:n.255-1535G>A

Variant summary

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

The ENST00000813851.1(ENSG00000305897):​n.255-1535G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,956 control chromosomes in the GnomAD database, including 28,418 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 0.60 (28418 hom., cov: 31)
• Consequence: ENSG00000305897 ENST00000813851.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.44
• Publications: 22 publications found

Genes affected

ENSG00000305897 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813851.1. 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
	ENSG00000305897	ENST00000813851.1		n.255-1535G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91818 AN: 151838 Hom.: 28391 Cov.: 31

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.605 AC: 91892 AN: 151956 Hom.: 28418 Cov.: 31 AF XY: 0.604 AC XY: 44877 AN XY: 74254

African (AFR) AF: 0.738 AC: 30609 AN: 41464

American (AMR) AF: 0.489 AC: 7464 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1960 AN: 3472

East Asian (EAS) AF: 0.525 AC: 2708 AN: 5156

South Asian (SAS) AF: 0.489 AC: 2347 AN: 4804

European-Finnish (FIN) AF: 0.629 AC: 6628 AN: 10536

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38384 AN: 67950

Other (OTH) AF: 0.559 AC: 1178 AN: 2108

Alfa AF: 0.571 Hom.: 74623

Bravo AF: 0.601

Asia WGS AF: 0.471 AC: 1641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.028
DANN	Benign	0.73
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs6137473; hg19: chr20-21884693;