ENST00000444086.1:n.29T>C

Variant names:

• chr10-68242351-A-G
• rs34888891
• ENST00000444086.1:n.29T>C

Variant summary

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

The ENST00000444086.1(LINC02640):​n.29T>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 0.133 in 152,144 control chromosomes in the GnomAD database, including 1,822 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 0.13 (1822 hom., cov: 32)
  • Exomes 𝑓: 0.20 (0 hom.)
• Consequence: LINC02640 ENST00000444086.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439
• Publications: 5 publications found

Genes affected

LINC02640 (HGNC:54123): (long intergenic non-protein coding RNA 2640)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444086.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02640	ENST00000444086.1	TSL:3	n.29T>C		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20259 AN: 152016 Hom.: 1819 Cov.: 32

Gnomad AFR AF: 0.0310

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.133

GnomAD4 exome AF: 0.200 AC: 2 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1 AN XY: 8

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: 0.250 AC: 2 AN: 8

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.133 AC: 20274 AN: 152134 Hom.: 1822 Cov.: 32 AF XY: 0.137 AC XY: 10209 AN XY: 74378

African (AFR) AF: 0.0309 AC: 1282 AN: 41542

American (AMR) AF: 0.209 AC: 3186 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 742 AN: 3468

East Asian (EAS) AF: 0.140 AC: 721 AN: 5158

South Asian (SAS) AF: 0.175 AC: 841 AN: 4812

European-Finnish (FIN) AF: 0.190 AC: 2008 AN: 10572

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10927 AN: 67990

Other (OTH) AF: 0.133 AC: 280 AN: 2108

Alfa AF: 0.148 Hom.: 885

Bravo AF: 0.132

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.73
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs34888891; hg19: chr10-70002108;