rs9468933

chr6-31297280-T-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_926691.3(LOC112267902):n.2357A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,242 control chromosomes in the GnomAD database, including 1,981 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 0.15 (1981 hom., cov: 32)
• Consequence: LOC112267902 XR_926691.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

Genes affected

LOC112267902 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267902	XR_926691.3	n.2357A>T		non_coding_transcript_exon_variant	5/5
LINC02571	NR_149115.1	n.167-2267A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02571	ENST00000539514.1	n.172-2267A>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23515 AN: 152124 Hom.: 1978 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.155 AC: 23528 AN: 152242 Hom.: 1981 Cov.: 32 AF XY: 0.155 AC XY: 11534 AN XY: 74434

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.174

Alfa AF: 0.156 Hom.: 262

Bravo AF: 0.157

Asia WGS AF: 0.134 AC: 466 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
Cadd	Benign	6.8
Dann	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9468933; hg19: chr6-31265057;