chr2-191155892-A-C

Position:

• chr2-191155892-A-C

Variant summary

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

The ENST00000623836.1(ENSG00000280083):​n.179T>G 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 0.566 in 152,100 control chromosomes in the GnomAD database, including 25,972 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 0.57 (25970 hom., cov: 32)
  • Exomes 𝑓: 0.44 (2 hom.)
• Consequence: ENSG00000280083 ENST00000623836.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902

Genes affected

ENSG00000280083 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.191155892A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000280083	ENST00000623836.1	n.179T>G		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86086 AN: 151964 Hom.: 25953 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.564

GnomAD4 exome AF: 0.444 AC: 8 AN: 18 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 6 AN XY: 12

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.566 AC: 86148 AN: 152082 Hom.: 25970 Cov.: 32 AF XY: 0.572 AC XY: 42524 AN XY: 74358

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.561

Alfa AF: 0.621 Hom.: 3849

Bravo AF: 0.556

Asia WGS AF: 0.543 AC: 1885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1031507; hg19: chr2-192020618;