10-7097556-G-T

Variant names:

• chr10-7097556-G-T
• rs3740215
• ENST00000420049.3:n.610G>T

Variant summary

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

The ENST00000420049.3(LINC02665):​n.610G>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 0.0679 in 152,260 control chromosomes in the GnomAD database, including 908 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 0.068 (908 hom., cov: 33)
  • Exomes 𝑓: 0.15 (0 hom.)
• Consequence: LINC02665 ENST00000420049.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682
• Publications: 1 publications found

Genes affected

LINC02665 (HGNC:54151): (long intergenic non-protein coding RNA 2665)

ENSG00000287277 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420049.3. 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
	LINC02665	NR_184104.1		n.534G>T		non_coding_transcript_exon	Exon 3 of 3
	LOC105376387	NR_188183.1		n.190+20724C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02665	ENST00000420049.3	TSL:3	n.610G>T		non_coding_transcript_exon	Exon 3 of 3
	LINC02665	ENST00000830756.1		n.505G>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000287277	ENST00000664549.1		n.190+20724C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0680 AC: 10342 AN: 152122 Hom.: 914 Cov.: 33

Gnomad AFR AF: 0.0615

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0226

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0346

Gnomad OTH AF: 0.0761

GnomAD4 exome AF: 0.150 AC: 3 AN: 20 Hom.: 0 Cov.: 0 AF XY: 0.143 AC XY: 2 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0833 AC: 1 AN: 12

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.0679 AC: 10343 AN: 152240 Hom.: 908 Cov.: 33 AF XY: 0.0712 AC XY: 5301 AN XY: 74440

African (AFR) AF: 0.0617 AC: 2564 AN: 41530

American (AMR) AF: 0.113 AC: 1729 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3472

East Asian (EAS) AF: 0.474 AC: 2447 AN: 5162

South Asian (SAS) AF: 0.126 AC: 611 AN: 4832

European-Finnish (FIN) AF: 0.0226 AC: 240 AN: 10604

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0346 AC: 2356 AN: 68022

Other (OTH) AF: 0.0753 AC: 159 AN: 2112

Alfa AF: 0.0293 Hom.: 38

Bravo AF: 0.0755

Asia WGS AF: 0.277 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.22
DANN	Benign	0.77
PhyloP100		-0.68

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: rs3740215;

hg19: chr10-7139518;