chr11-116649810-G-T

Position:

• chr11-116649810-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_135069.1(LINC02702):​n.117-3088G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,160 control chromosomes in the GnomAD database, including 3,444 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 0.21 (3444 hom., cov: 32)
• Consequence: LINC02702 NR_135069.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637

Genes affected

LINC02702 (HGNC:54217): (long intergenic non-protein coding RNA 2702)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02702	NR_135069.1	n.117-3088G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02702	ENST00000669244.1	n.77-3088G>T		intron_variant, non_coding_transcript_variant
LINC02702	ENST00000439483.2	n.59-3088G>T		intron_variant, non_coding_transcript_variant		2
LINC02702	ENST00000444123.5	n.117-3088G>T		intron_variant, non_coding_transcript_variant		5
LINC02702	ENST00000665087.1	n.31-3088G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31595 AN: 152042 Hom.: 3437 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.241

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.208 AC: 31627 AN: 152160 Hom.: 3444 Cov.: 32 AF XY: 0.207 AC XY: 15364 AN XY: 74398

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.248

Alfa AF: 0.224 Hom.: 4276

Bravo AF: 0.206

Asia WGS AF: 0.269 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.66
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1240773; hg19: chr11-116520527;