rs7120010

Positions:

• chr11-112277057-G-A
• chr11-112277057-G-T

Variant summary

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

The NR_126004.1(LINC02762):​n.35+6274G>A 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 0.141 in 152,162 control chromosomes in the GnomAD database, including 2,083 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 0.14 (2083 hom., cov: 33)
• Consequence: LINC02762 NR_126004.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

Genes affected

LINC02762 (HGNC:27443): (long intergenic non-protein coding RNA 2762)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02762	NR_126004.1	n.35+6274G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02762	ENST00000504610.2	n.35+6274G>A		intron_variant, non_coding_transcript_variant		2
LINC02762	ENST00000532168.3	n.37-3427G>A		intron_variant, non_coding_transcript_variant		3
LINC02762	ENST00000701675.1	n.37-3427G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21376 AN: 152044 Hom.: 2072 Cov.: 33

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0550

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.141 AC: 21415 AN: 152162 Hom.: 2083 Cov.: 33 AF XY: 0.138 AC XY: 10251 AN XY: 74402

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0550

Gnomad4 NFE AF: 0.0815

Gnomad4 OTH AF: 0.142

Alfa AF: 0.0833 Hom.: 528

Bravo AF: 0.148

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7120010; hg19: chr11-112147780;