rs9920421

Variant names:

• chr15-89824835-G-A
• rs9920421
• ENST00000727410.1:n.178+2189G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-89824835-G-A
• chr15-89824835-G-C

Variant summary

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

The ENST00000727410.1(ENSG00000295020):​n.178+2189G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,104 control chromosomes in the GnomAD database, including 37,454 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 0.70 (37454 hom., cov: 32)
• Consequence: ENSG00000295020 ENST00000727410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 18 publications found

Genes affected

ENSG00000295020 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727410.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295020	ENST00000727410.1		n.178+2189G>A		intron	N/A
	ENSG00000295020	ENST00000727411.1		n.213-587G>A		intron	N/A
	ENSG00000295020	ENST00000727412.1		n.190-587G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106384 AN: 151986 Hom.: 37410 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.700 AC: 106489 AN: 152104 Hom.: 37454 Cov.: 32 AF XY: 0.704 AC XY: 52320 AN XY: 74356

African (AFR) AF: 0.647 AC: 26823 AN: 41476

American (AMR) AF: 0.679 AC: 10381 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2593 AN: 3468

East Asian (EAS) AF: 0.794 AC: 4102 AN: 5164

South Asian (SAS) AF: 0.677 AC: 3268 AN: 4828

European-Finnish (FIN) AF: 0.742 AC: 7843 AN: 10574

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49119 AN: 67984

Other (OTH) AF: 0.712 AC: 1504 AN: 2112

Alfa AF: 0.714 Hom.: 47858

Bravo AF: 0.695

Asia WGS AF: 0.739 AC: 2569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.3
DANN	Benign	0.43
PhyloP100		1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9920421;

hg19: chr15-90368067;