chr6-17066364-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798149.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287359	ENST00000798149.1		n.225+27782A>T		intron	N/A
	ENSG00000287359	ENST00000798150.1		n.224+7802A>T		intron	N/A
	ENSG00000287359	ENST00000798151.1		n.212-5530A>T		intron	N/A

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 v4.9

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;