rs10484586

Positions:

• chr6-143001291-C-T

Variant summary

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

The NR_038987.1(LINC01277):​n.882+20375G>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 0.0526 in 152,278 control chromosomes in the GnomAD database, including 315 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 0.053 (315 hom., cov: 32)
• Consequence: LINC01277 NR_038987.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

LINC01277 (HGNC:50334): (long intergenic non-protein coding RNA 1277)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01277	NR_038987.1	n.882+20375G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01277	ENST00000446115.2	n.408-15161G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0526 AC: 8006 AN: 152160 Hom.: 314 Cov.: 32

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0361

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.0525

Gnomad SAS AF: 0.0532

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0526 AC: 8009 AN: 152278 Hom.: 315 Cov.: 32 AF XY: 0.0545 AC XY: 4060 AN XY: 74446

Gnomad4 AFR AF: 0.0119

Gnomad4 AMR AF: 0.0361

Gnomad4 ASJ AF: 0.0383

Gnomad4 EAS AF: 0.0528

Gnomad4 SAS AF: 0.0536

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.0708

Gnomad4 OTH AF: 0.0435

Alfa AF: 0.0637 Hom.: 177

Bravo AF: 0.0447

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.84
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: rs10484586; hg19: chr6-143322428;