chr21-24080388-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000287801 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.524 AC: 21698 AN: 41438

American (AMR) AF: 0.516 AC: 7859 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1846 AN: 3468

East Asian (EAS) AF: 0.352 AC: 1807 AN: 5134

South Asian (SAS) AF: 0.439 AC: 2113 AN: 4818

European-Finnish (FIN) AF: 0.404 AC: 4271 AN: 10560

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.521 AC: 35381 AN: 67882

Other (OTH) AF: 0.479 AC: 1009 AN: 2108

Alfa AF: 0.517 Hom.: 34530

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
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs2019006; hg19: chr21-25452702;