2-112842749-T-C

Position:

• chr2-112842749-T-C

Variant summary

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

The ENST00000623243.1(ENSG00000280228):​n.2422T>C 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 0.602 in 152,038 control chromosomes in the GnomAD database, including 28,021 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 0.60 (28007 hom., cov: 32)
  • Exomes 𝑓: 0.67 (14 hom.)
• Consequence: ENSG00000280228 ENST00000623243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

ENSG00000280228 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.112842749T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000280228	ENST00000623243.1	n.2422T>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91428 AN: 151860 Hom.: 27986 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.608

GnomAD4 exome AF: 0.667 AC: 40 AN: 60 Hom.: 14 Cov.: 0 AF XY: 0.674 AC XY: 31 AN XY: 46

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.761

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.602 AC: 91480 AN: 151978 Hom.: 28007 Cov.: 32 AF XY: 0.593 AC XY: 44077 AN XY: 74274

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.602

Alfa AF: 0.632 Hom.: 3822

Bravo AF: 0.597

Asia WGS AF: 0.463 AC: 1609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13013349; hg19: chr2-113600326;