17-50001585-A-G

Variant summary

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

The ENST00000511867.1(ENSG00000248172):n.139+4558A>G 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 0.879 in 152,222 control chromosomes in the GnomAD database, including 59,565 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 0.88 (59565 hom., cov: 32)
• Consequence: ENST00000511867.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 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
	ENST00000511867.1	n.139+4558A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133703 AN: 152104 Hom.: 59547 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.879 AC: 133770 AN: 152222 Hom.: 59565 Cov.: 32 AF XY: 0.880 AC XY: 65520 AN XY: 74436

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.882

Alfa AF: 0.930 Hom.: 96049

Bravo AF: 0.869

Asia WGS AF: 0.913 AC: 3174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.7
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1991293; hg19: chr17-48078949;