rs1014263

Positions:

• chr17-39004193-A-G
• chr17-39004193-A-T

Variant summary

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

The ENST00000583161.1(ENSG00000266588):​n.165-474T>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 0.104 in 151,938 control chromosomes in the GnomAD database, including 1,467 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 0.10 (1467 hom., cov: 31)
• Consequence: ENST00000583161.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 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
	ENST00000583161.1	n.165-474T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15736 AN: 151818 Hom.: 1456 Cov.: 31

Gnomad AFR AF: 0.0259

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0903

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0928

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.104 AC: 15755 AN: 151938 Hom.: 1467 Cov.: 31 AF XY: 0.110 AC XY: 8134 AN XY: 74248

Gnomad4 AFR AF: 0.0259

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0903

Gnomad4 NFE AF: 0.0929

Gnomad4 OTH AF: 0.109

Alfa AF: 0.106 Hom.: 1815

Bravo AF: 0.118

Asia WGS AF: 0.229 AC: 796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1014263; hg19: chr17-37160446;