17-6004123-A-T

Variant names:

• chr17-6004123-A-T
• rs9303196
• ENST00000573619.1:c.-289+14102A>T

Variant summary

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

The ENST00000573619.1(ENSG00000285471):​c.-289+14102A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,148 control chromosomes in the GnomAD database, including 48,993 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 0.80 (48993 hom., cov: 32)
• Consequence: ENSG00000285471 ENST00000573619.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

Genes affected

ENSG00000285471 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285471	ENST00000573619.1	c.-289+14102A>T		intron_variant	Intron 4 of 4	2		ENSP00000461865.1

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121417 AN: 152030 Hom.: 48959 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.799 AC: 121495 AN: 152148 Hom.: 48993 Cov.: 32 AF XY: 0.801 AC XY: 59576 AN XY: 74384

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.870

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.914

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.832

Alfa AF: 0.829 Hom.: 28962

Bravo AF: 0.801

Asia WGS AF: 0.869 AC: 3022 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	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9303196; hg19: chr17-5907443;