8-11762477-C-T

Variant names:

• chr8-11762477-C-T
• rs7015453
• NR_171032.1:n.1222C>T

Variant summary

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

The NR_171032.1(LINC02905):​n.1222C>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 0.25 in 191,220 control chromosomes in the GnomAD database, including 6,853 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 0.25 (5321 hom., cov: 31)
  • Exomes 𝑓: 0.25 (1532 hom.)
• Consequence: LINC02905 NR_171032.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 8 publications found

Genes affected

LINC02905 (HGNC:32200): (long intergenic non-protein coding RNA 2905)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_171032.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02905	NR_171032.1		n.1222C>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38121 AN: 151698 Hom.: 5320 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.228

GnomAD4 exome AF: 0.246 AC: 9674 AN: 39404 Hom.: 1532 Cov.: 0 AF XY: 0.249 AC XY: 5115 AN XY: 20570

African (AFR) AF: 0.331 AC: 422 AN: 1276

American (AMR) AF: 0.241 AC: 849 AN: 3530

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 80 AN: 780

East Asian (EAS) AF: 0.530 AC: 1446 AN: 2730

South Asian (SAS) AF: 0.337 AC: 1656 AN: 4908

European-Finnish (FIN) AF: 0.218 AC: 271 AN: 1244

Middle Eastern (MID) AF: 0.196 AC: 27 AN: 138

European-Non Finnish (NFE) AF: 0.197 AC: 4501 AN: 22816

Other (OTH) AF: 0.213 AC: 422 AN: 1982

GnomAD4 genome AF: 0.251 AC: 38149 AN: 151816 Hom.: 5321 Cov.: 31 AF XY: 0.256 AC XY: 18989 AN XY: 74200

African (AFR) AF: 0.321 AC: 13264 AN: 41330

American (AMR) AF: 0.232 AC: 3530 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3470

East Asian (EAS) AF: 0.536 AC: 2765 AN: 5162

South Asian (SAS) AF: 0.337 AC: 1625 AN: 4818

European-Finnish (FIN) AF: 0.234 AC: 2465 AN: 10514

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13449 AN: 67968

Other (OTH) AF: 0.229 AC: 483 AN: 2110

Alfa AF: 0.184 Hom.: 1010

Bravo AF: 0.252

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.66
PhyloP100		-0.61
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7015453; hg19: chr8-11619986;