rs6028335

chr20-39216834-A-G

Variant summary

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

The NR_027124.1(LINC01734):n.195-722T>C 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 0.163 in 152,120 control chromosomes in the GnomAD database, including 2,438 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 0.16 (2438 hom., cov: 32)
• Consequence: LINC01734 NR_027124.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

Genes affected

LINC01734 (HGNC:52522): (long intergenic non-protein coding RNA 1734)

LOC107985448 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01734	NR_027124.1	n.195-722T>C		intron_variant, non_coding_transcript_variant
LOC107985448	XR_001754587.1	n.148-2753A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01734	ENST00000412672.1	n.195-722T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24824 AN: 152002 Hom.: 2440 Cov.: 32

Gnomad AFR AF: 0.0589

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.163 AC: 24825 AN: 152120 Hom.: 2438 Cov.: 32 AF XY: 0.164 AC XY: 12180 AN XY: 74366

Gnomad4 AFR AF: 0.0589

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.0947

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.185

Alfa AF: 0.215 Hom.: 6946

Bravo AF: 0.159

Asia WGS AF: 0.141 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.84
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6028335; hg19: chr20-37845477;