11-1051715-T-C

Position:

• chr11-1051715-T-C

Variant summary

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

The XM_047427955.1(LOC124902605):​c.-1671T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,040 control chromosomes in the GnomAD database, including 25,779 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 0.57 (25756 hom., cov: 32)
  • Exomes 𝑓: 0.59 (23 hom.)
• Consequence: LOC124902605 XM_047427955.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549

Genes affected

LOC124902605 (HGNC:):

LINC02688 (HGNC:54184): (long intergenic non-protein coding RNA 2688)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902605	XM_047427955.1	c.-1671T>C		5_prime_UTR_variant	3/4		XP_047283911.1
LINC02688	NR_160890.1	n.176T>C		non_coding_transcript_exon_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02688	ENST00000534584.2	n.176T>C		non_coding_transcript_exon_variant	2/4	3

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87194 AN: 151802 Hom.: 25709 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.559

GnomAD4 exome AF: 0.592 AC: 71 AN: 120 Hom.: 23 Cov.: 0 AF XY: 0.600 AC XY: 54 AN XY: 90

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.583

Gnomad4 NFE exome AF: 0.609

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.575 AC: 87291 AN: 151920 Hom.: 25756 Cov.: 32 AF XY: 0.573 AC XY: 42535 AN XY: 74254

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.562

Alfa AF: 0.543 Hom.: 21857

Bravo AF: 0.566

Asia WGS AF: 0.599 AC: 2086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10794359; hg19: chr11-1051715;