chr10-118359086-T-C

Variant names:

• chr10-118359086-T-C
• rs236212
• ENST00000411666.6:n.368T>C

Variant summary

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

The ENST00000445161.5(LINC00867):​n.463T>C 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 0.196 in 152,258 control chromosomes in the GnomAD database, including 3,140 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 0.20 (3140 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LINC00867 ENST00000445161.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.727
• Publications: 4 publications found

Genes affected

LINC00867 (HGNC:45265): (long intergenic non-protein coding RNA 867)

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 (AMR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445161.5. 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
	LINC00867	NR_108045.1		n.463T>C		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00867	ENST00000411666.6	TSL:3	n.368T>C		non_coding_transcript_exon	Exon 4 of 4
	LINC00867	ENST00000445161.5	TSL:2	n.463T>C		non_coding_transcript_exon	Exon 3 of 3
	LINC00867	ENST00000664512.2		n.739T>C		non_coding_transcript_exon	Exon 4 of 5

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29783 AN: 152138 Hom.: 3139 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.202

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.196 AC: 29791 AN: 152256 Hom.: 3140 Cov.: 32 AF XY: 0.196 AC XY: 14573 AN XY: 74438

African (AFR) AF: 0.105 AC: 4346 AN: 41564

American (AMR) AF: 0.264 AC: 4030 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 605 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1298 AN: 5176

South Asian (SAS) AF: 0.186 AC: 897 AN: 4830

European-Finnish (FIN) AF: 0.169 AC: 1787 AN: 10604

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16179 AN: 68004

Other (OTH) AF: 0.204 AC: 432 AN: 2116

Alfa AF: 0.225 Hom.: 18214

Bravo AF: 0.202

Asia WGS AF: 0.202 AC: 705 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	8.7
DANN	Benign	0.58
PhyloP100		0.73

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: rs236212;

hg19: chr10-120118598;