2-6629186-C-T

Variant names:

• chr2-6629186-C-T
• rs7584788
• ENST00000455317.5:n.165-2948G>A

Variant summary

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

The ENST00000455317.5(MIR7515HG):​n.165-2948G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,124 control chromosomes in the GnomAD database, including 1,679 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 0.14 (1679 hom., cov: 32)
• Consequence: MIR7515HG ENST00000455317.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 3 publications found

Genes affected

MIR7515HG (HGNC:49838): (MIR7515 host gene)

LINC01246 (HGNC:49840): (long intergenic non-protein coding RNA 1246)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455317.5. 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
	LINC01246	NR_110498.1		n.414-2948G>A		intron	N/A
	LINC01246	NR_110500.1		n.165-2948G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR7515HG	ENST00000455317.5	TSL:2	n.165-2948G>A		intron	N/A
	MIR7515HG	ENST00000456028.5	TSL:4	n.414-2948G>A		intron	N/A
	MIR7515HG	ENST00000585781.6	TSL:5	n.1391-2948G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21845 AN: 152006 Hom.: 1683 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.144 AC: 21845 AN: 152124 Hom.: 1679 Cov.: 32 AF XY: 0.142 AC XY: 10599 AN XY: 74382

African (AFR) AF: 0.187 AC: 7756 AN: 41480

American (AMR) AF: 0.163 AC: 2489 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 675 AN: 3470

East Asian (EAS) AF: 0.0207 AC: 107 AN: 5172

South Asian (SAS) AF: 0.120 AC: 578 AN: 4816

European-Finnish (FIN) AF: 0.115 AC: 1221 AN: 10594

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8596 AN: 67988

Other (OTH) AF: 0.145 AC: 307 AN: 2114

Alfa AF: 0.134 Hom.: 759

Bravo AF: 0.150

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.22
PhyloP100		-0.94

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: rs7584788;

hg19: chr2-6769318;