chr2-199678-A-G

Variant names:

• chr2-199678-A-G
• rs385909
• ENST00000437798.1:n.2110A>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227061	ENST00000437798.1	n.2110A>G		non_coding_transcript_exon_variant	Exon 1 of 2	1
ENSG00000227061	ENST00000653001.1	n.128-486A>G		intron_variant	Intron 1 of 2
ENSG00000227061	ENST00000665534.1	n.111-66A>G		intron_variant	Intron 1 of 4

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;