chr2-199678-A-G

Position:

• chr2-199678-A-G

Variant summary

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

The ENST00000437798.1(ENSG00000227061):​n.2110A>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 0.776 in 152,258 control chromosomes in the GnomAD database, including 47,341 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 0.78 (47337 hom., cov: 35)
  • Exomes 𝑓: 1.0 (4 hom.)
• Consequence: ENSG00000227061 ENST00000437798.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512

Genes affected

ENSG00000227061 (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 (SAS) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.199678A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000227061	ENST00000437798.1	n.2110A>G		non_coding_transcript_exon_variant	1/2	1
ENSG00000227061	ENST00000653001.1	n.128-486A>G		intron_variant
ENSG00000227061	ENST00000665534.1	n.111-66A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.776 AC: 118122 AN: 152132 Hom.: 47336 Cov.: 35

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.786

GnomAD4 exome AF: 1.00 AC: 8 AN: 8 Hom.: 4 Cov.: 0 AF XY: 1.00 AC XY: 4 AN XY: 4

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.776 AC: 118145 AN: 152250 Hom.: 47337 Cov.: 35 AF XY: 0.778 AC XY: 57915 AN XY: 74450

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.830

Gnomad4 NFE AF: 0.872

Gnomad4 OTH AF: 0.784

Alfa AF: 0.852 Hom.: 36784

Bravo AF: 0.765

Asia WGS AF: 0.830 AC: 2886 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	3.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs385909; hg19: chr2-199678;