17-6004123-A-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

Genes affected

ENSG00000285471 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000573619.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285471	ENST00000573619.1	TSL:2	c.-289+14102A>T		intron	N/A	ENSP00000461865.1	I3NI40

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

African (AFR) AF: 0.685 AC: 28409 AN: 41474

American (AMR) AF: 0.870 AC: 13310 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3059 AN: 3470

East Asian (EAS) AF: 0.914 AC: 4726 AN: 5170

South Asian (SAS) AF: 0.815 AC: 3933 AN: 4824

European-Finnish (FIN) AF: 0.817 AC: 8655 AN: 10596

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56614 AN: 68004

Other (OTH) AF: 0.832 AC: 1757 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.40
PhyloP100		-0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9303196;

hg19: chr17-5907443;