rs2280509

Positions:

• chr2-202032645-C-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: ENST00000691022.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000691022.1	n.574C>T		non_coding_transcript_exon_variant	1/1

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;