6-68275038-T-G

Position:

• chr6-68275038-T-G

Variant summary

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

The NR_125854.1(LINC02549):​n.238-8423A>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 0.231 in 151,906 control chromosomes in the GnomAD database, including 4,811 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 0.23 (4811 hom., cov: 32)
• Consequence: LINC02549 NR_125854.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.694

Genes affected

LINC02549 (HGNC:53584): (long intergenic non-protein coding RNA 2549)

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 = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02549	NR_125854.1	n.238-8423A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02549	ENST00000445346.1	n.238-8423A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34982 AN: 151788 Hom.: 4796 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.231 AC: 35017 AN: 151906 Hom.: 4811 Cov.: 32 AF XY: 0.226 AC XY: 16766 AN XY: 74220

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.189

Alfa AF: 0.194 Hom.: 4927

Bravo AF: 0.234

Asia WGS AF: 0.0850 AC: 297 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10455657; hg19: chr6-68984930;