rs7717092

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-152496901-G-A
• chr5-152496901-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000286749 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.878

Gnomad4 EAS AF: 0.947

Gnomad4 SAS AF: 0.910

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.842

Gnomad4 OTH AF: 0.842

Alfa AF: 0.844 Hom.: 67430

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7717092; hg19: chr5-151876462;