chr6-31294661-C-T

Position:

• chr6-31294661-C-T

Variant summary

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

The NR_149115.1(LINC02571):​n.236+283G>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 0.354 in 151,970 control chromosomes in the GnomAD database, including 9,729 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 0.35 (9729 hom., cov: 32)
• Consequence: LINC02571 NR_149115.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72

Genes affected

LINC02571 (HGNC:53630): (long intergenic non-protein coding RNA 2571)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02571	NR_149115.1	n.236+283G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1	n.241+283G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53686 AN: 151852 Hom.: 9719 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.354 AC: 53724 AN: 151970 Hom.: 9729 Cov.: 32 AF XY: 0.360 AC XY: 26715 AN XY: 74286

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.355

Alfa AF: 0.309 Hom.: 7829

Bravo AF: 0.353

Asia WGS AF: 0.366 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3873380; hg19: chr6-31262438;