2-150987464-T-C

Variant summary

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

The ENST00000425983.1(ENSG00000228064):n.10+4949T>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 0.872 in 152,172 control chromosomes in the GnomAD database, including 58,510 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 0.87 (58510 hom., cov: 32)
• Consequence: ENST00000425983.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 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
	ENST00000425983.1	n.10+4949T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132661 AN: 152054 Hom.: 58468 Cov.: 32

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.872 AC: 132757 AN: 152172 Hom.: 58510 Cov.: 32 AF XY: 0.875 AC XY: 65047 AN XY: 74368

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.914

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.961

Gnomad4 NFE AF: 0.922

Gnomad4 OTH AF: 0.877

Alfa AF: 0.911 Hom.: 5739

Bravo AF: 0.865

Asia WGS AF: 0.884 AC: 3074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.0
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs989414; hg19: chr2-151843978;