rs875430

chr11-109744932-C-T

Variant summary

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

The ENST00000662064.1(LINC02715):n.441+20G>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 0.0838 in 152,246 control chromosomes in the GnomAD database, including 619 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 0.084 (619 hom., cov: 33)
• Consequence: LINC02715 ENST00000662064.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22

Genes affected

LINC02715 (HGNC:54232): (long intergenic non-protein coding RNA 2715)

LOC124902751 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902751	XR_007062883.1	n.139+20G>A		intron_variant, non_coding_transcript_variant
LOC124902751	XR_007062882.1	n.139+20G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02715	ENST00000662064.1	n.441+20G>A		intron_variant, non_coding_transcript_variant
LINC02715	ENST00000667432.1	n.551+20G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0838 AC: 12755 AN: 152128 Hom.: 619 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0781

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0824

Gnomad OTH AF: 0.0895

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

GnomAD4 genome AF: 0.0838 AC: 12762 AN: 152246 Hom.: 619 Cov.: 33 AF XY: 0.0805 AC XY: 5991 AN XY: 74452

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0779

Gnomad4 ASJ AF: 0.0824

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0458

Gnomad4 FIN AF: 0.0331

Gnomad4 NFE AF: 0.0824

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.0834 Hom.: 724

Bravo AF: 0.0885

Asia WGS AF: 0.0260 AC: 93 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.13
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: rs875430; hg19: chr11-109615658;