chr6-31294392-T-C

Variant names:

• chr6-31294392-T-C
• rs3873379
• ENST00000539514.1:n.242-97A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000539514.1(LINC02571):​n.242-97A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,080 control chromosomes in the GnomAD database, including 9,570 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 (9570 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC02571 ENST00000539514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 38 publications found

Genes affected

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

ENSG00000298396 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02571	NR_149115.1	n.237-97A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1	n.242-97A>G		intron_variant	Intron 2 of 3	4
ENSG00000298396	ENST00000755297.1	n.32+23286T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53090 AN: 151962 Hom.: 9558 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.349 AC: 53133 AN: 152080 Hom.: 9570 Cov.: 32 AF XY: 0.352 AC XY: 26197 AN XY: 74360

African (AFR) AF: 0.446 AC: 18489 AN: 41472

American (AMR) AF: 0.334 AC: 5095 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3466

East Asian (EAS) AF: 0.307 AC: 1586 AN: 5174

South Asian (SAS) AF: 0.331 AC: 1593 AN: 4816

European-Finnish (FIN) AF: 0.392 AC: 4151 AN: 10588

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20099 AN: 67980

Other (OTH) AF: 0.344 AC: 724 AN: 2106

Alfa AF: 0.312 Hom.: 32724

Bravo AF: 0.348

Asia WGS AF: 0.311 AC: 1083 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	6.8
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3873379; hg19: chr6-31262169;