2-232586209-C-T

Variant summary

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

The ENST00000415506.6(ENSG00000237126):n.409+483G>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 0.759 in 151,898 control chromosomes in the GnomAD database, including 44,078 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 0.76 (44075 hom., cov: 30)
  • Exomes 𝑓: 0.75 (3 hom.)
• Consequence: ENST00000415506.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.799 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
	ENST00000415506.6	n.409+483G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115236 AN: 151772 Hom.: 44040 Cov.: 30

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.726

GnomAD4 exome AF: 0.750 AC: 6 AN: 8 Hom.: 3 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 NFE exome AF: 0.750

GnomAD4 genome AF: 0.759 AC: 115323 AN: 151890 Hom.: 44075 Cov.: 30 AF XY: 0.760 AC XY: 56415 AN XY: 74232

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.728

Alfa AF: 0.742 Hom.: 10106

Bravo AF: 0.747

Asia WGS AF: 0.762 AC: 2651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.8
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2276560; hg19: chr2-233450919;