chr11-78426005-T-C

Position:

• chr11-78426005-T-C

Variant summary

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

The NR_120564.1(LINC02728):​n.360-600A>G 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 0.056 in 152,290 control chromosomes in the GnomAD database, including 379 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 0.056 (379 hom., cov: 32)
• Consequence: LINC02728 NR_120564.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279

Genes affected

LINC02728 (HGNC:54245): (long intergenic non-protein coding RNA 2728)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02728	NR_120564.1	n.360-600A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02728	ENST00000513207.2	n.360-600A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000534168.1	n.36-17643T>C		intron_variant, non_coding_transcript_variant		3
LINC02728	ENST00000660634.1	n.659-600A>G		intron_variant, non_coding_transcript_variant
LINC02728	ENST00000664831.1	n.503-600A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0560 AC: 8520 AN: 152172 Hom.: 378 Cov.: 32

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.0462

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0997

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0799

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0560 AC: 8521 AN: 152290 Hom.: 379 Cov.: 32 AF XY: 0.0562 AC XY: 4185 AN XY: 74464

Gnomad4 AFR AF: 0.0134

Gnomad4 AMR AF: 0.0461

Gnomad4 ASJ AF: 0.0531

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0468

Gnomad4 FIN AF: 0.0997

Gnomad4 NFE AF: 0.0799

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0606 Hom.: 160

Bravo AF: 0.0509

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34956708; hg19: chr11-78137051;