21-24082863-T-C

Variant names:

• chr21-24082863-T-C
• rs1910662
• ENST00000668921.1:n.137+31353A>G

Variant summary

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

The ENST00000668921.1(ENSG00000287801):​n.137+31353A>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 151,980 control chromosomes in the GnomAD database, including 19,661 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 (19661 hom., cov: 32)
• Consequence: ENSG00000287801 ENST00000668921.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

ENSG00000287801 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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+31353A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76746 AN: 151862 Hom.: 19646 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.396

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: 76802 AN: 151980 Hom.: 19661 Cov.: 32 AF XY: 0.497 AC XY: 36940 AN XY: 74278

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.479

Alfa AF: 0.516 Hom.: 26592

Bravo AF: 0.514

Asia WGS AF: 0.415 AC: 1443 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1910662; hg19: chr21-25455176;