chr11-34574061-G-A

Variant names:

• chr11-34574061-G-A
• rs1530966
• XR_931181.3:n.110-272G>A

Variant summary

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

The XR_931181.3(LINC02707):​n.110-272G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,854 control chromosomes in the GnomAD database, including 8,359 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 0.32 (8358 hom., cov: 30)
  • Exomes 𝑓: 0.18 (1 hom.)
• Consequence: LINC02707 XR_931181.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400
• Publications: 3 publications found

Genes affected

LINC02707 (HGNC:54224): (long intergenic non-protein coding RNA 2707)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527135.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02707	ENST00000527135.1	TSL:4	n.*79G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48549 AN: 151676 Hom.: 8337 Cov.: 30

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.0507

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.316

GnomAD4 exome AF: 0.183 AC: 11 AN: 60 Hom.: 1 AF XY: 0.237 AC XY: 9 AN XY: 38

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.179 AC: 10 AN: 56

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.320 AC: 48602 AN: 151794 Hom.: 8358 Cov.: 30 AF XY: 0.311 AC XY: 23094 AN XY: 74190

African (AFR) AF: 0.427 AC: 17663 AN: 41332

American (AMR) AF: 0.227 AC: 3463 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3466

East Asian (EAS) AF: 0.0508 AC: 262 AN: 5158

South Asian (SAS) AF: 0.118 AC: 566 AN: 4794

European-Finnish (FIN) AF: 0.305 AC: 3210 AN: 10536

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21410 AN: 67940

Other (OTH) AF: 0.312 AC: 657 AN: 2106

Alfa AF: 0.311 Hom.: 9776

Bravo AF: 0.320

Asia WGS AF: 0.110 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.55
PhyloP100		0.40
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1530966; hg19: chr11-34595608;