13-86836360-G-A

Variant names:

• chr13-86836360-G-A
• rs4495987
• ENST00000720455.1:n.258+5880C>T

Variant summary

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

The ENST00000720455.1(ENSG00000294000):​n.258+5880C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 151,994 control chromosomes in the GnomAD database, including 5,827 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 0.27 (5827 hom., cov: 32)
• Consequence: ENSG00000294000 ENST00000720455.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 1 publications found

Genes affected

ENSG00000294000 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370300	XR_931621.3	n.361+41384G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294000	ENST00000720455.1	n.258+5880C>T		intron_variant	Intron 2 of 3
ENSG00000294000	ENST00000720456.1	n.121+14396C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41331 AN: 151876 Hom.: 5817 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.272 AC: 41368 AN: 151994 Hom.: 5827 Cov.: 32 AF XY: 0.276 AC XY: 20471 AN XY: 74290

African (AFR) AF: 0.292 AC: 12123 AN: 41450

American (AMR) AF: 0.338 AC: 5157 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 715 AN: 3472

East Asian (EAS) AF: 0.425 AC: 2190 AN: 5156

South Asian (SAS) AF: 0.387 AC: 1863 AN: 4808

European-Finnish (FIN) AF: 0.220 AC: 2323 AN: 10572

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.238 AC: 16176 AN: 67956

Other (OTH) AF: 0.258 AC: 544 AN: 2106

Alfa AF: 0.246 Hom.: 610

Bravo AF: 0.281

Asia WGS AF: 0.371 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4495987; hg19: chr13-87488615;