rs2829644

Variant names:

• chr21-25214010-A-G
• rs2829644
• ENST00000409758.1:n.90-38565T>C

Variant summary

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

The ENST00000409758.1(ENSG00000222042):​n.90-38565T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0589 in 152,132 control chromosomes in the GnomAD database, including 308 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 0.059 (308 hom., cov: 32)
• Consequence: ENSG00000222042 ENST00000409758.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

Genes affected

ENSG00000222042 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 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
ENSG00000222042	ENST00000409758.1	n.90-38565T>C		intron_variant	Intron 1 of 3	3
ENSG00000222042	ENST00000656005.1	n.218-38565T>C		intron_variant	Intron 2 of 4
ENSG00000222042	ENST00000667825.1	n.190-38565T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0589 AC: 8955 AN: 152014 Hom.: 309 Cov.: 32

Gnomad AFR AF: 0.0423

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0376

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0479

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0619

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0589 AC: 8953 AN: 152132 Hom.: 308 Cov.: 32 AF XY: 0.0598 AC XY: 4450 AN XY: 74368

Gnomad4 AFR AF: 0.0422

Gnomad4 AMR AF: 0.0376

Gnomad4 ASJ AF: 0.0764

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0479

Gnomad4 NFE AF: 0.0619

Gnomad4 OTH AF: 0.0596

Alfa AF: 0.0624 Hom.: 464

Bravo AF: 0.0545

Asia WGS AF: 0.166 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2829644; hg19: chr21-26586324;