5-13088300-C-G

Variant names:

• chr5-13088300-C-G
• rs1840870
• ENST00000782146.1:n.120-19811C>G

Variant summary

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

The ENST00000782146.1(ENSG00000301839):​n.120-19811C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,030 control chromosomes in the GnomAD database, including 37,819 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 0.69 (37819 hom., cov: 32)
• Consequence: ENSG00000301839 ENST00000782146.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835
• Publications: 1 publications found

Genes affected

ENSG00000301839 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782146.1. 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
	ENSG00000301839	ENST00000782146.1		n.120-19811C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104817 AN: 151912 Hom.: 37767 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.690 AC: 104926 AN: 152030 Hom.: 37819 Cov.: 32 AF XY: 0.694 AC XY: 51532 AN XY: 74280

African (AFR) AF: 0.890 AC: 36958 AN: 41534

American (AMR) AF: 0.613 AC: 9361 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2087 AN: 3468

East Asian (EAS) AF: 0.895 AC: 4629 AN: 5170

South Asian (SAS) AF: 0.608 AC: 2932 AN: 4822

European-Finnish (FIN) AF: 0.715 AC: 7553 AN: 10558

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39226 AN: 67898

Other (OTH) AF: 0.670 AC: 1414 AN: 2110

Alfa AF: 0.552 Hom.: 1749

Bravo AF: 0.690

Asia WGS AF: 0.721 AC: 2503 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.34
DANN	Benign	0.28
PhyloP100		-0.83

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: rs1840870;

hg19: chr5-13088412;