rs360234

chr2-126283978-C-T

Variant summary

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

The ENST00000703015.1(ENSG00000290113):n.356+24022G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 151,960 control chromosomes in the GnomAD database, including 47,027 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 (47027 hom., cov: 30)
• Consequence: ENST00000703015.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000703015.1	n.356+24022G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117749 AN: 151844 Hom.: 46983 Cov.: 30

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.775 AC: 117845 AN: 151960 Hom.: 47027 Cov.: 30 AF XY: 0.768 AC XY: 57059 AN XY: 74264

Gnomad4 AFR AF: 0.947

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.761

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.751

Alfa AF: 0.746 Hom.: 43492

Bravo AF: 0.773

Asia WGS AF: 0.502 AC: 1745 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.034
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs360234; hg19: chr2-127041555;