ENST00000668921.1:n.137+33828A>G

Variant names:

• chr21-24080388-T-C
• rs2019006
• ENST00000668921.1:n.137+33828A>G

Variant summary

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

The ENST00000668921.1(ENSG00000287801):​n.137+33828A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 151,836 control chromosomes in the GnomAD database, including 19,635 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 0.51 (19635 hom., cov: 31)
• Consequence: ENSG00000287801 ENST00000668921.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907

Genes affected

ENSG00000287801 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 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
ENSG00000287801	ENST00000668921.1	n.137+33828A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76680 AN: 151718 Hom.: 19620 Cov.: 31

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.505 AC: 76736 AN: 151836 Hom.: 19635 Cov.: 31 AF XY: 0.497 AC XY: 36890 AN XY: 74204

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.479

Alfa AF: 0.516 Hom.: 24755

Bravo AF: 0.514

Asia WGS AF: 0.416 AC: 1446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2019006; hg19: chr21-25452702;