rs427469

Variant names:

• chr2-126280699-T-C
• rs360231
• ENST00000703015.1:n.356+27301A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-126280699-T-C
• chrNW_018654709.1-91572-T-C

Variant summary

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

The ENST00000703015.1(ENSG00000290113):​n.356+27301A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 151,938 control chromosomes in the GnomAD database, including 11,751 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 0.38 (11751 hom., cov: 32)
• Consequence: ENSG00000290113 ENST00000703015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713

Genes affected

ENSG00000290113 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 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
ENSG00000290113	ENST00000703015.1	n.356+27301A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57829 AN: 151820 Hom.: 11725 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.381 AC: 57904 AN: 151938 Hom.: 11751 Cov.: 32 AF XY: 0.377 AC XY: 27992 AN XY: 74234

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.371

Alfa AF: 0.370 Hom.: 1354

Bravo AF: 0.384

Asia WGS AF: 0.237 AC: 825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs360231; hg19: chr2-127038276;