chr2-112842838-C-T

Position:

• chr2-112842838-C-T

Variant summary

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

The ENST00000623243.1(ENSG00000280228):​n.2511C>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 0.379 in 152,124 control chromosomes in the GnomAD database, including 11,611 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 0.38 (11608 hom., cov: 32)
  • Exomes 𝑓: 0.35 (3 hom.)
• Consequence: ENSG00000280228 ENST00000623243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

Genes affected

ENSG00000280228 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.112842838C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000280228	ENST00000623243.1	n.2511C>T		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57661 AN: 151946 Hom.: 11613 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.387

GnomAD4 exome AF: 0.350 AC: 21 AN: 60 Hom.: 3 Cov.: 0 AF XY: 0.345 AC XY: 20 AN XY: 58

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.375

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.379 AC: 57656 AN: 152064 Hom.: 11608 Cov.: 32 AF XY: 0.376 AC XY: 27963 AN XY: 74334

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.382

Alfa AF: 0.393 Hom.: 2274

Bravo AF: 0.375

Asia WGS AF: 0.330 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13032029; hg19: chr2-113600415;