rs2835345

Variant names:

• chr21-36429136-C-A
• rs2835345
• ENST00000691257.1:n.*210G>T

Your query was ambiguous. Multiple possible variants found:

• chr21-36429136-C-A
• chr21-36429136-C-T

Variant summary

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

The ENST00000691257.1(ENSG00000289221):​n.*210G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,018 control chromosomes in the GnomAD database, including 4,854 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 0.24 (4854 hom., cov: 32)
• Consequence: ENSG00000289221 ENST00000691257.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

ENSG00000289221 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 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
ENSG00000289221	ENST00000691257.1	n.*210G>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35787 AN: 151900 Hom.: 4848 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.236 AC: 35806 AN: 152018 Hom.: 4854 Cov.: 32 AF XY: 0.244 AC XY: 18122 AN XY: 74290

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.238

Alfa AF: 0.243 Hom.: 1147

Bravo AF: 0.235

Asia WGS AF: 0.322 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2835345; hg19: chr21-37801434;