rs9380240

chr6-31301055-T-C

Variant summary

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

The NR_149115.1(LINC02571):n.166+417A>G 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 0.473 in 151,850 control chromosomes in the GnomAD database, including 17,487 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 0.47 (17487 hom., cov: 31)
• Consequence: LINC02571 NR_149115.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

Genes affected

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

LOC112267902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02571	NR_149115.1	n.166+417A>G		intron_variant, non_coding_transcript_variant
LOC112267902	XR_926691.3	n.1060+704A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02571	ENST00000539514.1	n.171+417A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71803 AN: 151732 Hom.: 17464 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.473 AC: 71878 AN: 151850 Hom.: 17487 Cov.: 31 AF XY: 0.484 AC XY: 35886 AN XY: 74220

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.497

Alfa AF: 0.417 Hom.: 10987

Bravo AF: 0.477

Asia WGS AF: 0.618 AC: 2148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	3.2
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9380240; hg19: chr6-31268832;