rs2280509

Variant names:

• chr2-202032645-C-T
• rs2280509
• ENST00000691022.1:n.574C>T

Variant summary

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

The ENST00000691022.1(ENSG00000289026):​n.574C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,216 control chromosomes in the GnomAD database, including 2,070 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 0.14 (2067 hom., cov: 32)
  • Exomes 𝑓: 0.26 (3 hom.)
• Consequence: ENSG00000289026 ENST00000691022.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798

Genes affected

ENSG00000289026 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.333 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
ENSG00000289026	ENST00000691022.1	n.574C>T		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000273209	ENST00000608741.1	n.*125G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22070 AN: 152034 Hom.: 2073 Cov.: 32

Gnomad AFR AF: 0.0458

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.158

GnomAD4 exome AF: 0.258 AC: 16 AN: 62 Hom.: 3 AF XY: 0.273 AC XY: 12 AN XY: 44

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.208

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.145 AC: 22059 AN: 152154 Hom.: 2067 Cov.: 32 AF XY: 0.146 AC XY: 10889 AN XY: 74374

Gnomad4 AFR AF: 0.0458

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.159

Alfa AF: 0.146 Hom.: 256

Bravo AF: 0.141

Asia WGS AF: 0.320 AC: 1113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2280509; hg19: chr2-202897368;