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. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000290113 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000290113	ENST00000797885.1	n.335+27301A>G		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.507 AC: 21002 AN: 41400

American (AMR) AF: 0.299 AC: 4567 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1001 AN: 3468

East Asian (EAS) AF: 0.295 AC: 1518 AN: 5152

South Asian (SAS) AF: 0.165 AC: 797 AN: 4822

European-Finnish (FIN) AF: 0.386 AC: 4076 AN: 10570

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23677 AN: 67954

Other (OTH) AF: 0.371 AC: 783 AN: 2112

Alfa AF: 0.376 Hom.: 1456

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
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs360231; hg19: chr2-127038276;