rs34198350

Positions:

• chr2-47942243-C-T

Variant summary

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

The ENST00000447571.5(ENSG00000230773):​n.1261G>A 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 0.0945 in 152,320 control chromosomes in the GnomAD database, including 772 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 0.094 (771 hom., cov: 32)
  • Exomes 𝑓: 0.14 (1 hom.)
• Consequence: ENSG00000230773 ENST00000447571.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

Genes affected

ENSG00000230773 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.47942243C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230773	ENST00000447571.5	n.1261G>A		non_coding_transcript_exon_variant	9/9	1
ENSG00000230773	ENST00000651429.1	n.807+6724G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0944 AC: 14362 AN: 152084 Hom.: 766 Cov.: 32

Gnomad AFR AF: 0.0830

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.0377

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0195

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.0936

GnomAD4 exome AF: 0.136 AC: 16 AN: 118 Hom.: 1 Cov.: 0 AF XY: 0.146 AC XY: 14 AN XY: 96

Gnomad4 AFR exome AF: 0.100

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.143

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0945 AC: 14383 AN: 152202 Hom.: 771 Cov.: 32 AF XY: 0.0933 AC XY: 6943 AN XY: 74410

Gnomad4 AFR AF: 0.0833

Gnomad4 AMR AF: 0.0630

Gnomad4 ASJ AF: 0.0377

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.0922

Alfa AF: 0.107 Hom.: 174

Bravo AF: 0.0868

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34198350; hg19: chr2-48169382;