2-46651212-C-G

Variant summary

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

The XR_940058.3(LOC105374584):n.3234C>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 0.309 in 152,134 control chromosomes in the GnomAD database, including 7,806 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 0.31 (7806 hom., cov: 33)
• Consequence: LOC105374584 XR_940058.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

Genes affected

LOC105374584 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374584	XR_940058.3	n.3234C>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.309 AC: 47033 AN: 152016 Hom.: 7798 Cov.: 33

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0975

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.289

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.309 AC: 47073 AN: 152134 Hom.: 7806 Cov.: 33 AF XY: 0.309 AC XY: 23019 AN XY: 74380

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.0971

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.286

Alfa AF: 0.137 Hom.: 212

Bravo AF: 0.319

Asia WGS AF: 0.219 AC: 761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	5.0
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13406427; hg19: chr2-46878351;