rs219722

Variant names:

• chr21-26385450-A-C
• rs219722
• ENST00000429340.1:n.226-1551A>C

Your query was ambiguous. Multiple possible variants found:

• chr21-26385450-A-C
• chr21-26385450-A-G
• chr21-26385450-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429340.1(ENSG00000232692):​n.226-1551A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 151,330 control chromosomes in the GnomAD database, including 59,486 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 0.89 (59486 hom., cov: 30)
• Consequence: ENSG00000232692 ENST00000429340.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.494

Genes affected

ENSG00000232692 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 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
ENSG00000232692	ENST00000429340.1	n.226-1551A>C		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134003 AN: 151218 Hom.: 59459 Cov.: 30

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.886 AC: 134083 AN: 151330 Hom.: 59486 Cov.: 30 AF XY: 0.886 AC XY: 65570 AN XY: 73988

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.898

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.883

Alfa AF: 0.896 Hom.: 7584

Bravo AF: 0.882

Asia WGS AF: 0.861 AC: 2983 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs219722; hg19: chr21-27757769;