rs1477268

Variant names:

• chr5-87132049-T-C
• rs1477268
• ENST00000503349.1:n.344-5405T>C

Variant summary

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

The ENST00000503349.1(ENSG00000249061):​n.344-5405T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,116 control chromosomes in the GnomAD database, including 3,997 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 0.23 (3997 hom., cov: 33)
• Consequence: ENSG00000249061 ENST00000503349.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 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.48-5405T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249061	ENST00000503349.1	TSL:2	n.344-5405T>C		intron	N/A
	ENSG00000249061	ENST00000515750.1	TSL:5	n.48-5405T>C		intron	N/A
	MIR4280HG	ENST00000662995.1		n.149-3504A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34781 AN: 151998 Hom.: 3998 Cov.: 33

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.229 AC: 34792 AN: 152116 Hom.: 3997 Cov.: 33 AF XY: 0.228 AC XY: 16946 AN XY: 74372

African (AFR) AF: 0.251 AC: 10413 AN: 41466

American (AMR) AF: 0.233 AC: 3556 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3472

East Asian (EAS) AF: 0.236 AC: 1224 AN: 5178

South Asian (SAS) AF: 0.212 AC: 1025 AN: 4826

European-Finnish (FIN) AF: 0.218 AC: 2307 AN: 10590

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14856 AN: 67980

Other (OTH) AF: 0.210 AC: 444 AN: 2112

Alfa AF: 0.221 Hom.: 2169

Bravo AF: 0.231

Asia WGS AF: 0.217 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.60
DANN	Benign	0.68
PhyloP100		-0.35

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: rs1477268;

hg19: chr5-86427866;