6-31298745-G-T

Position:

• chr6-31298745-G-T

Variant summary

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

The ENST00000539514.1(LINC02571):​n.171+2727C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 151,800 control chromosomes in the GnomAD database, including 32,215 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 0.65 (32215 hom., cov: 30)
• Consequence: LINC02571 ENST00000539514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

LINC02571 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02571	NR_149115.1	n.166+2727C>A		intron_variant
LOC112267902	XR_926691.3	n.1061-169C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1	n.171+2727C>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98411 AN: 151682 Hom.: 32173 Cov.: 30

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.649 AC: 98505 AN: 151800 Hom.: 32215 Cov.: 30 AF XY: 0.653 AC XY: 48471 AN XY: 74172

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.679

Alfa AF: 0.609 Hom.: 53084

Bravo AF: 0.656

Asia WGS AF: 0.751 AC: 2609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2524089; hg19: chr6-31266522;