ENST00000587628.6:n.1911G>A

Variant names:

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

Variant summary

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

The ENST00000587628.6(MIR7515HG):​n.1911G>A 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 0.0691 in 152,010 control chromosomes in the GnomAD database, including 705 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 0.069 (705 hom., cov: 32)
• Consequence: MIR7515HG ENST00000587628.6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01246	NR_110498.1	n.113-225G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR7515HG	ENST00000587628.6	n.1911G>A		non_coding_transcript_exon_variant	Exon 8 of 8	5
MIR7515HG	ENST00000656553.1	n.1594G>A		non_coding_transcript_exon_variant	Exon 7 of 7
MIR7515HG	ENST00000456028.5	n.113-225G>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.0691 AC: 10497 AN: 151892 Hom.: 707 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.0201

Gnomad SAS AF: 0.0653

Gnomad FIN AF: 0.0234

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0674

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

GnomAD4 genome AF: 0.0691 AC: 10506 AN: 152010 Hom.: 705 Cov.: 32 AF XY: 0.0700 AC XY: 5197 AN XY: 74278

African (AFR) AF: 0.168 AC: 6972 AN: 41448

American (AMR) AF: 0.0913 AC: 1393 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3468

East Asian (EAS) AF: 0.0199 AC: 103 AN: 5166

South Asian (SAS) AF: 0.0639 AC: 308 AN: 4820

European-Finnish (FIN) AF: 0.0234 AC: 248 AN: 10582

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.0181 AC: 1228 AN: 67958

Other (OTH) AF: 0.0667 AC: 141 AN: 2114

Alfa AF: 0.0881 Hom.: 231

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.062
DANN	Benign	0.52
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6714052; hg19: chr2-6774326;