rs219724

chr21-26385622-C-T

Variant summary

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

The ENST00000429340.1(ENSG00000232692):n.226-1379C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,114 control chromosomes in the GnomAD database, including 59,162 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 0.88 (59162 hom., cov: 30)
• Consequence: ENST00000429340.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000429340.1	n.226-1379C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.881 AC: 133968 AN: 151996 Hom.: 59121 Cov.: 30

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.882

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.881 AC: 134067 AN: 152114 Hom.: 59162 Cov.: 30 AF XY: 0.882 AC XY: 65604 AN XY: 74372

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.885

Gnomad4 FIN AF: 0.893

Gnomad4 NFE AF: 0.890

Gnomad4 OTH AF: 0.874

Alfa AF: 0.884 Hom.: 58761

Bravo AF: 0.876

Asia WGS AF: 0.864 AC: 3006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.5
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs219724; hg19: chr21-27757941;