rs7120010

Variant names:

• chr11-112277057-G-A
• rs7120010
• ENST00000729087.1:n.490G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000729087.1(LINC02762):​n.490G>A 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 0.141 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 ENST00000729087.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02762	NR_126004.1	n.35+6274G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02762	ENST00000729087.1	n.490G>A		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02762	ENST00000504610.2	n.35+6274G>A		intron_variant	Intron 1 of 3	2
LINC02762	ENST00000532168.4	n.78-3427G>A		intron_variant	Intron 1 of 2	3

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

African (AFR) AF: 0.279 AC: 11585 AN: 41456

American (AMR) AF: 0.105 AC: 1611 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3470

East Asian (EAS) AF: 0.105 AC: 545 AN: 5178

South Asian (SAS) AF: 0.150 AC: 724 AN: 4818

European-Finnish (FIN) AF: 0.0550 AC: 583 AN: 10608

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0815 AC: 5540 AN: 68016

Other (OTH) AF: 0.142 AC: 300 AN: 2110

Alfa AF: 0.0949 Hom.: 922

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs7120010; hg19: chr11-112147780;