5-87136800-T-C

Variant names:

• chr5-87136800-T-C
• rs2032794
• ENST00000503349.1:n.344-654T>C

Variant summary

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

The ENST00000503349.1(ENSG00000249061):​n.344-654T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,132 control chromosomes in the GnomAD database, including 2,659 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 0.17 (2659 hom., cov: 31)
• Consequence: ENSG00000249061 ENST00000503349.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662
• Publications: 10 publications found

Genes affected

ENSG00000249061 (HGNC:):

MIR4280HG (HGNC:54975): (MIR4280 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503349.1. 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
	LOC101929380	NR_105018.1		n.48-654T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249061	ENST00000503349.1	TSL:2	n.344-654T>C		intron	N/A
	ENSG00000249061	ENST00000515750.1	TSL:5	n.48-654T>C		intron	N/A
	MIR4280HG	ENST00000662995.1		n.148+1450A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25522 AN: 152016 Hom.: 2659 Cov.: 31

Gnomad AFR AF: 0.0400

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.168 AC: 25515 AN: 152132 Hom.: 2659 Cov.: 31 AF XY: 0.170 AC XY: 12655 AN XY: 74376

African (AFR) AF: 0.0399 AC: 1656 AN: 41542

American (AMR) AF: 0.209 AC: 3197 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 793 AN: 3472

East Asian (EAS) AF: 0.237 AC: 1221 AN: 5156

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4814

European-Finnish (FIN) AF: 0.218 AC: 2304 AN: 10580

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14823 AN: 67978

Other (OTH) AF: 0.163 AC: 345 AN: 2114

Alfa AF: 0.199 Hom.: 6869

Bravo AF: 0.162

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	3.7
DANN	Benign	0.91
PhyloP100		0.66

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: rs2032794;

hg19: chr5-86432617;