rs4406273

chr6-31298313-G-Achr6-31298313-G-T

Variant summary

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

The XR_926691.3(LOC112267902):n.1324C>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 0.0861 in 152,196 control chromosomes in the GnomAD database, including 594 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 0.086 (594 hom., cov: 32)
• Consequence: LOC112267902 XR_926691.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

Genes affected

LOC112267902 (HGNC:):

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267902	XR_926691.3	n.1324C>T		non_coding_transcript_exon_variant	5/5
LINC02571	NR_149115.1	n.166+3159C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02571	ENST00000539514.1	n.171+3159C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0861 AC: 13096 AN: 152078 Hom.: 592 Cov.: 32

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0418

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0606

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0916

Gnomad OTH AF: 0.0900

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

GnomAD4 genome AF: 0.0861 AC: 13100 AN: 152196 Hom.: 594 Cov.: 32 AF XY: 0.0857 AC XY: 6374 AN XY: 74406

Gnomad4 AFR AF: 0.0909

Gnomad4 AMR AF: 0.0638

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0419

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0606

Gnomad4 NFE AF: 0.0916

Gnomad4 OTH AF: 0.0876

Alfa AF: 0.0824 Hom.: 198

Bravo AF: 0.0865

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.3
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4406273; hg19: chr6-31266090; COSMIC: COSV73434407;