5-152497196-G-A

Variant names:

• chr5-152497196-G-A
• rs7717550
• ENST00000663460.1:n.217-40508G>A

Variant summary

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

The ENST00000663460.1(ENSG00000286749):​n.217-40508G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 152,050 control chromosomes in the GnomAD database, including 51,213 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 (51213 hom., cov: 32)
• Consequence: ENSG00000286749 ENST00000663460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663460.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286749	ENST00000663460.1		n.217-40508G>A		intron	N/A
	ENSG00000286749	ENST00000663819.1		n.184-40508G>A		intron	N/A
	ENSG00000286749	ENST00000812686.1		n.152-40508G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124236 AN: 151932 Hom.: 51170 Cov.: 32

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.875

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: 0.835

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

GnomAD4 genome AF: 0.818 AC: 124332 AN: 152050 Hom.: 51213 Cov.: 32 AF XY: 0.822 AC XY: 61109 AN XY: 74330

African (AFR) AF: 0.709 AC: 29412 AN: 41458

American (AMR) AF: 0.875 AC: 13358 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.878 AC: 3049 AN: 3472

East Asian (EAS) AF: 0.947 AC: 4901 AN: 5176

South Asian (SAS) AF: 0.910 AC: 4389 AN: 4824

European-Finnish (FIN) AF: 0.872 AC: 9226 AN: 10584

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

European-Non Finnish (NFE) AF: 0.842 AC: 57198 AN: 67952

Other (OTH) AF: 0.837 AC: 1765 AN: 2108

Alfa AF: 0.826 Hom.: 21210

Bravo AF: 0.815

Asia WGS AF: 0.915 AC: 3181 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.42
DANN	Benign	0.58
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs7717550; hg19: chr5-151876757;