5-87909191-T-C

Variant names:

• chr5-87909191-T-C
• rs1358572
• ENST00000655360.1:n.388-41315A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655360.1(ENSG00000287862):​n.388-41315A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,112 control chromosomes in the GnomAD database, including 2,773 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 0.13 (2773 hom., cov: 32)
• Consequence: ENSG00000287862 ENST00000655360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730

Genes affected

ENSG00000287862 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 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
ENSG00000287862	ENST00000655360.1	n.388-41315A>G		intron_variant	Intron 2 of 2
ENSG00000287862	ENST00000668454.1	n.219-41312A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19844 AN: 151994 Hom.: 2764 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.0423

Gnomad FIN AF: 0.0445

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0398

Gnomad OTH AF: 0.0942

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

GnomAD4 genome AF: 0.131 AC: 19880 AN: 152112 Hom.: 2773 Cov.: 32 AF XY: 0.127 AC XY: 9425 AN XY: 74386

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.0891

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.0419

Gnomad4 FIN AF: 0.0445

Gnomad4 NFE AF: 0.0398

Gnomad4 OTH AF: 0.0960

Alfa AF: 0.0934 Hom.: 215

Bravo AF: 0.143

Asia WGS AF: 0.0570 AC: 197 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1358572; hg19: chr5-87205008;