ENST00000726471.1:n.403+19394A>G

Variant names:

• chr21-31068221-T-C
• rs1475591
• ENST00000726471.1:n.403+19394A>G

Variant summary

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

The ENST00000726471.1(ENSG00000294875):​n.403+19394A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 152,232 control chromosomes in the GnomAD database, including 56,781 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 0.85 (56781 hom., cov: 33)
• Consequence: ENSG00000294875 ENST00000726471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 8 publications found

Genes affected

ENSG00000294875 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.95 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
ENSG00000294875	ENST00000726471.1	n.403+19394A>G		intron_variant	Intron 1 of 2
ENSG00000294875	ENST00000726472.1	n.403+19394A>G		intron_variant	Intron 1 of 1
ENSG00000294875	ENST00000726473.1	n.333+14818A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129075 AN: 152114 Hom.: 56772 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.848 AC: 129120 AN: 152232 Hom.: 56781 Cov.: 33 AF XY: 0.850 AC XY: 63247 AN XY: 74436

African (AFR) AF: 0.586 AC: 24329 AN: 41494

American (AMR) AF: 0.923 AC: 14126 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3262 AN: 3472

East Asian (EAS) AF: 0.917 AC: 4744 AN: 5174

South Asian (SAS) AF: 0.899 AC: 4333 AN: 4822

European-Finnish (FIN) AF: 0.964 AC: 10236 AN: 10618

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.956 AC: 65060 AN: 68032

Other (OTH) AF: 0.883 AC: 1868 AN: 2116

Alfa AF: 0.930 Hom.: 164670

Bravo AF: 0.837

Asia WGS AF: 0.893 AC: 3105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.032
DANN	Benign	0.42
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1475591; hg19: chr21-32440540;