12-30215524-T-C

Variant summary

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

The ENST00000549055.1(ENSG00000257262):n.258-2079T>C 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 0.533 in 151,792 control chromosomes in the GnomAD database, including 21,808 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 0.53 (21808 hom., cov: 33)
• Consequence: ENST00000549055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.621 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
	ENST00000549055.1	n.258-2079T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80855 AN: 151676 Hom.: 21787 Cov.: 33

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.533 AC: 80926 AN: 151792 Hom.: 21808 Cov.: 33 AF XY: 0.532 AC XY: 39448 AN XY: 74166

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.548

Alfa AF: 0.567 Hom.: 50031

Bravo AF: 0.540

Asia WGS AF: 0.547 AC: 1901 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	2.3
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10843660; hg19: chr12-30368457;