rs10877887

Variant names:

• chr12-62603400-T-C
• rs10877887
• ENST00000408887.3:n.291A>G

Variant summary

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

The NR_121682.1(LINC01465):​n.35A>G 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 0.412 in 1,189,168 control chromosomes in the GnomAD database, including 101,417 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 0.42 (13471 hom., cov: 32)
  • Exomes 𝑓: 0.41 (87946 hom.)
• Consequence: LINC01465 NR_121682.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 49 publications found

Genes affected

LINC01465 (HGNC:26364): (long intergenic non-protein coding RNA 1465)

ENSG00000275180 (HGNC:):

MIRLET7IHG (HGNC:55478): (MIRLET7I host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_121682.1. 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
	LINC01465	NR_121682.1		n.35A>G		non_coding_transcript_exon	Exon 1 of 1
	MIRLET7IHG	NR_186001.1		n.93+565T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01465	ENST00000408887.3	TSL:6	n.291A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000275180	ENST00000619323.3	TSL:6	n.208T>C		non_coding_transcript_exon	Exon 1 of 1
	MIRLET7IHG	ENST00000550290.2	TSL:4	n.84+565T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63409 AN: 151790 Hom.: 13463 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.423

GnomAD4 exome AF: 0.411 AC: 426123 AN: 1037262 Hom.: 87946 Cov.: 23 AF XY: 0.411 AC XY: 205462 AN XY: 500336

African (AFR) AF: 0.477 AC: 8753 AN: 18358

American (AMR) AF: 0.343 AC: 4627 AN: 13482

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 4751 AN: 9486

East Asian (EAS) AF: 0.356 AC: 3328 AN: 9348

South Asian (SAS) AF: 0.392 AC: 24273 AN: 61906

European-Finnish (FIN) AF: 0.362 AC: 5023 AN: 13890

Middle Eastern (MID) AF: 0.442 AC: 1020 AN: 2310

European-Non Finnish (NFE) AF: 0.412 AC: 358996 AN: 871696

Other (OTH) AF: 0.417 AC: 15352 AN: 36786

GnomAD4 genome AF: 0.418 AC: 63441 AN: 151906 Hom.: 13471 Cov.: 32 AF XY: 0.413 AC XY: 30684 AN XY: 74274

African (AFR) AF: 0.481 AC: 19920 AN: 41418

American (AMR) AF: 0.370 AC: 5663 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1741 AN: 3468

East Asian (EAS) AF: 0.347 AC: 1774 AN: 5108

South Asian (SAS) AF: 0.389 AC: 1878 AN: 4822

European-Finnish (FIN) AF: 0.377 AC: 3987 AN: 10570

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.400 AC: 27151 AN: 67910

Other (OTH) AF: 0.418 AC: 883 AN: 2114

Alfa AF: 0.402 Hom.: 1566

Bravo AF: 0.421

Asia WGS AF: 0.330 AC: 1143 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.33
PhyloP100		-0.57
Mutation Taster		=300/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10877887; hg19: chr12-62997180;