rs6714052

Variant names:

• chr2-6634194-C-A
• rs6714052
• ENST00000587628.6:n.1911G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-6634194-C-A
• chr2-6634194-C-T

Variant summary

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

The ENST00000656553.1(MIR7515HG):​n.1594G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0742 in 151,998 control chromosomes in the GnomAD database, including 550 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 0.074 (550 hom., cov: 32)
• Consequence: MIR7515HG ENST00000656553.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656553.1. 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
	LINC01246	NR_110498.1		n.113-225G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR7515HG	ENST00000587628.6	TSL:5	n.1911G>T		non_coding_transcript_exon	Exon 8 of 8
	MIR7515HG	ENST00000656553.1		n.1594G>T		non_coding_transcript_exon	Exon 7 of 7
	MIR7515HG	ENST00000456028.5	TSL:4	n.113-225G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0743 AC: 11280 AN: 151880 Hom.: 552 Cov.: 32

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0560

Gnomad FIN AF: 0.0915

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.0742 AC: 11271 AN: 151998 Hom.: 550 Cov.: 32 AF XY: 0.0723 AC XY: 5368 AN XY: 74274

African (AFR) AF: 0.0185 AC: 766 AN: 41460

American (AMR) AF: 0.0713 AC: 1087 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3470

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5166

South Asian (SAS) AF: 0.0562 AC: 271 AN: 4818

European-Finnish (FIN) AF: 0.0915 AC: 967 AN: 10572

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.108 AC: 7336 AN: 67946

Other (OTH) AF: 0.0795 AC: 168 AN: 2114

Alfa AF: 0.0100 Hom.: 231

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.053
DANN	Benign	0.46
PhyloP100		-2.0

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: rs6714052;

hg19: chr2-6774326;