rs2853923

Positions:

• chr6-31297960-A-G
• chr6-31297960-A-T

Variant summary

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

The XR_926691.3(LOC112267902):​n.1677T>C 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 0.498 in 152,056 control chromosomes in the GnomAD database, including 19,058 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 0.50 (19058 hom., cov: 32)
• Consequence: LOC112267902 XR_926691.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267902	XR_926691.3	n.1677T>C		non_coding_transcript_exon_variant	5/5
LINC02571	NR_149115.1	n.167-2947T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02571	ENST00000539514.1	n.172-2947T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75650 AN: 151938 Hom.: 19044 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.498 AC: 75697 AN: 152056 Hom.: 19058 Cov.: 32 AF XY: 0.500 AC XY: 37125 AN XY: 74318

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.511

Alfa AF: 0.447 Hom.: 14951

Bravo AF: 0.502

Asia WGS AF: 0.600 AC: 2088 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	3.0
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: rs2853923; hg19: chr6-31265737;