chr20-48450711-A-G

Variant names:

• chr20-48450711-A-G
• rs926693
• ENST00000814081.1:n.197-16A>G

Variant summary

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

The ENST00000814081.1(ENSG00000305916):​n.197-16A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,962 control chromosomes in the GnomAD database, including 26,467 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 0.58 (26467 hom., cov: 32)
• Consequence: ENSG00000305916 ENST00000814081.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 3 publications found

Genes affected

ENSG00000305916 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 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
ENSG00000305916	ENST00000814081.1	n.197-16A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87617 AN: 151844 Hom.: 26408 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.577 AC: 87732 AN: 151962 Hom.: 26467 Cov.: 32 AF XY: 0.582 AC XY: 43178 AN XY: 74244

African (AFR) AF: 0.721 AC: 29852 AN: 41430

American (AMR) AF: 0.659 AC: 10070 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1586 AN: 3470

East Asian (EAS) AF: 0.776 AC: 3993 AN: 5144

South Asian (SAS) AF: 0.611 AC: 2942 AN: 4814

European-Finnish (FIN) AF: 0.463 AC: 4893 AN: 10568

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32540 AN: 67932

Other (OTH) AF: 0.550 AC: 1160 AN: 2110

Alfa AF: 0.486 Hom.: 8773

Bravo AF: 0.599

Asia WGS AF: 0.644 AC: 2239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.070
DANN	Benign	0.48
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs926693; hg19: chr20-47078957;