6-468597-A-G

Variant names:

• chr6-468597-A-G
• rs13205238
• ENST00000661640.1:n.336-6611A>G

Variant summary

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

The ENST00000661640.1(ENSG00000286364):​n.336-6611A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 151,548 control chromosomes in the GnomAD database, including 48,011 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 0.78 (48011 hom., cov: 29)
• Consequence: ENSG00000286364 ENST00000661640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.19
• Publications: 4 publications found

Genes affected

ENSG00000286364 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.896 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
ENSG00000286364	ENST00000661640.1	n.336-6611A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118259 AN: 151430 Hom.: 47982 Cov.: 29

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.961

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.781 AC: 118347 AN: 151548 Hom.: 48011 Cov.: 29 AF XY: 0.780 AC XY: 57706 AN XY: 74016

African (AFR) AF: 0.551 AC: 22709 AN: 41190

American (AMR) AF: 0.776 AC: 11839 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3025 AN: 3468

East Asian (EAS) AF: 0.707 AC: 3631 AN: 5134

South Asian (SAS) AF: 0.739 AC: 3552 AN: 4806

European-Finnish (FIN) AF: 0.905 AC: 9423 AN: 10410

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61335 AN: 67980

Other (OTH) AF: 0.811 AC: 1701 AN: 2098

Alfa AF: 0.844 Hom.: 70521

Bravo AF: 0.763

Asia WGS AF: 0.707 AC: 2460 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	0.23
DANN	Benign	0.43
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs13205238; hg19: chr6-468597;