ENST00000663460.1:n.217-40803G>A

Variant names:

• chr5-152496901-G-A
• rs7717092
• ENST00000663460.1:n.217-40803G>A

Variant summary

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

The ENST00000663460.1(ENSG00000286749):​n.217-40803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,060 control chromosomes in the GnomAD database, including 52,308 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 0.83 (52308 hom., cov: 32)
• Consequence: ENSG00000286749 ENST00000663460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 3 publications found

Genes affected

ENSG00000286749 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 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
ENSG00000286749	ENST00000663460.1	n.217-40803G>A		intron_variant	Intron 1 of 3
ENSG00000286749	ENST00000663819.1	n.184-40803G>A		intron_variant	Intron 1 of 3
ENSG00000286749	ENST00000812686.1	n.152-40803G>A		intron_variant	Intron 2 of 4
ENSG00000286749	ENST00000812687.1	n.186-40803G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125721 AN: 151942 Hom.: 52265 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.827 AC: 125819 AN: 152060 Hom.: 52308 Cov.: 32 AF XY: 0.832 AC XY: 61824 AN XY: 74346

African (AFR) AF: 0.744 AC: 30844 AN: 41476

American (AMR) AF: 0.877 AC: 13407 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.878 AC: 3040 AN: 3462

East Asian (EAS) AF: 0.947 AC: 4909 AN: 5182

South Asian (SAS) AF: 0.910 AC: 4390 AN: 4826

European-Finnish (FIN) AF: 0.872 AC: 9235 AN: 10590

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.842 AC: 57187 AN: 67930

Other (OTH) AF: 0.842 AC: 1773 AN: 2106

Alfa AF: 0.841 Hom.: 158309

Bravo AF: 0.827

Asia WGS AF: 0.918 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.24
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs7717092; hg19: chr5-151876462;