21-15313279-A-G

Variant names:

• chr21-15313279-A-G
• rs722098
• ENST00000769434.1:n.387-1925A>G

Variant summary

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

The ENST00000769434.1(ENSG00000300143):​n.387-1925A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 152,098 control chromosomes in the GnomAD database, including 16,271 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 0.39 (16271 hom., cov: 32)
• Consequence: ENSG00000300143 ENST00000769434.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 30 publications found

Genes affected

ENSG00000300143 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000769434.1. 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
	ENSG00000300143	ENST00000769434.1		n.387-1925A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59656 AN: 151980 Hom.: 16217 Cov.: 32

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.393 AC: 59772 AN: 152098 Hom.: 16271 Cov.: 32 AF XY: 0.401 AC XY: 29831 AN XY: 74336

African (AFR) AF: 0.749 AC: 31075 AN: 41490

American (AMR) AF: 0.437 AC: 6671 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3466

East Asian (EAS) AF: 0.532 AC: 2751 AN: 5168

South Asian (SAS) AF: 0.346 AC: 1664 AN: 4814

European-Finnish (FIN) AF: 0.291 AC: 3077 AN: 10566

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12636 AN: 67998

Other (OTH) AF: 0.352 AC: 743 AN: 2110

Alfa AF: 0.282 Hom.: 15704

Bravo AF: 0.420

Asia WGS AF: 0.453 AC: 1575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.024
DANN	Benign	0.53
PhyloP100		-1.9

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: rs722098;

hg19: chr21-16685598;

COSMIC: COSV50192791;