rs4495987

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr13-86836360-G-A
• chr13-86836360-G-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720455.1. 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
	ENSG00000294000	ENST00000720455.1		n.258+5880C>T		intron	N/A
	ENSG00000294000	ENST00000720456.1		n.121+14396C>T		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs4495987;

hg19: chr13-87488615;