20-21899407-A-G

Variant names:

• chr20-21899407-A-G
• rs1998076
• ENST00000813851.1:n.254+3473A>G

Variant summary

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

The ENST00000813851.1(ENSG00000305897):​n.254+3473A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,110 control chromosomes in the GnomAD database, including 31,579 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 0.64 (31579 hom., cov: 33)
• Consequence: ENSG00000305897 ENST00000813851.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674
• Publications: 15 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 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
ENSG00000305897	ENST00000813851.1	n.254+3473A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96680 AN: 151992 Hom.: 31548 Cov.: 33

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.636 AC: 96763 AN: 152110 Hom.: 31579 Cov.: 33 AF XY: 0.635 AC XY: 47178 AN XY: 74336

African (AFR) AF: 0.789 AC: 32749 AN: 41506

American (AMR) AF: 0.517 AC: 7906 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2088 AN: 3472

East Asian (EAS) AF: 0.601 AC: 3098 AN: 5158

South Asian (SAS) AF: 0.497 AC: 2395 AN: 4820

European-Finnish (FIN) AF: 0.634 AC: 6705 AN: 10578

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39922 AN: 67984

Other (OTH) AF: 0.590 AC: 1243 AN: 2108

Alfa AF: 0.599 Hom.: 86586

Bravo AF: 0.635

Asia WGS AF: 0.513 AC: 1786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.57
DANN	Benign	0.54
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1998076; hg19: chr20-21880045;