2-59436771-C-T

Variant summary

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

The ENST00000412409.3(ENSG00000233891):n.545+158034G>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 0.0509 in 152,030 control chromosomes in the GnomAD database, including 277 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 0.051 (277 hom., cov: 32)
• Consequence: ENST00000412409.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.101 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
	ENST00000412409.3	n.545+158034G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000606382.1	n.433+75238G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000648110.1	n.733-1128C>T		intron_variant, non_coding_transcript_variant
	ENST00000415159.1	n.151+1408C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0509 AC: 7729 AN: 151912 Hom.: 273 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0984

Gnomad ASJ AF: 0.0776

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.0246

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0509 AC: 7741 AN: 152030 Hom.: 277 Cov.: 32 AF XY: 0.0514 AC XY: 3817 AN XY: 74308

Gnomad4 AFR AF: 0.0700

Gnomad4 AMR AF: 0.0989

Gnomad4 ASJ AF: 0.0776

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.0293

Gnomad4 FIN AF: 0.0246

Gnomad4 NFE AF: 0.0283

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0263 Hom.: 13

Bravo AF: 0.0611

Asia WGS AF: 0.0630 AC: 221 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.0
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: rs10490056; hg19: chr2-59663906;