6-17066364-T-A

Variant names:

• chr6-17066364-T-A
• rs9383242
• ENST00000798149.1:n.225+27782A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000798149.1(ENSG00000287359):​n.225+27782A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,102 control chromosomes in the GnomAD database, including 52,695 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 0.82 (52695 hom., cov: 32)
• Consequence: ENSG00000287359 ENST00000798149.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 2 publications found

Genes affected

ENSG00000287359 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901269	XR_007059481.1	n.39-5530A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287359	ENST00000798149.1	n.225+27782A>T		intron_variant	Intron 1 of 1
ENSG00000287359	ENST00000798150.1	n.224+7802A>T		intron_variant	Intron 2 of 2
ENSG00000287359	ENST00000798151.1	n.212-5530A>T		intron_variant	Intron 1 of 1
ENSG00000287359	ENST00000798152.1	n.487-5530A>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125142 AN: 151986 Hom.: 52674 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.823 AC: 125206 AN: 152102 Hom.: 52695 Cov.: 32 AF XY: 0.827 AC XY: 61517 AN XY: 74352

African (AFR) AF: 0.627 AC: 26005 AN: 41446

American (AMR) AF: 0.857 AC: 13076 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3144 AN: 3466

East Asian (EAS) AF: 0.994 AC: 5150 AN: 5182

South Asian (SAS) AF: 0.909 AC: 4376 AN: 4816

European-Finnish (FIN) AF: 0.914 AC: 9703 AN: 10614

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60895 AN: 68000

Other (OTH) AF: 0.852 AC: 1800 AN: 2112

Alfa AF: 0.856 Hom.: 7022

Bravo AF: 0.808

Asia WGS AF: 0.935 AC: 3252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.50
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs9383242; hg19: chr6-17066595;