rs1158292

Variant names:

• chr5-63689606-G-A
• rs1158292
• ENST00000722712.1:n.391+8199C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-63689606-G-A
• chr5-63689606-G-T

Variant summary

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

The ENST00000722712.1(ENSG00000294317):​n.391+8199C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,892 control chromosomes in the GnomAD database, including 7,291 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 0.28 (7291 hom., cov: 31)
• Consequence: ENSG00000294317 ENST00000722712.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 2 publications found

Genes affected

ENSG00000294317 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722712.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294317	ENST00000722712.1		n.391+8199C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43102 AN: 151774 Hom.: 7291 Cov.: 31

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.284 AC: 43104 AN: 151892 Hom.: 7291 Cov.: 31 AF XY: 0.292 AC XY: 21654 AN XY: 74234

African (AFR) AF: 0.104 AC: 4316 AN: 41446

American (AMR) AF: 0.333 AC: 5077 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2490 AN: 5108

South Asian (SAS) AF: 0.392 AC: 1890 AN: 4816

European-Finnish (FIN) AF: 0.445 AC: 4695 AN: 10544

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.336 AC: 22817 AN: 67948

Other (OTH) AF: 0.287 AC: 606 AN: 2108

Alfa AF: 0.242 Hom.: 1179

Bravo AF: 0.267

Asia WGS AF: 0.397 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.65
PhyloP100		0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1158292;

hg19: chr5-62985433;