chr6-31297537-T-C

Variant names:

• chr6-31297537-T-C
• rs2524123
• XR_926691.3:n.2100A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_926691.3(LOC112267902):​n.2100A>G 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 0.339 in 151,940 control chromosomes in the GnomAD database, including 8,996 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 0.34 (8996 hom., cov: 31)
• Consequence: LOC112267902 XR_926691.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 27 publications found

Genes affected

LOC112267902 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000539514.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02571	NR_149115.1		n.167-2524A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02571	ENST00000539514.1	TSL:4	n.172-2524A>G		intron	N/A
	ENSG00000298396	ENST00000755297.1		n.32+26431T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51454 AN: 151822 Hom.: 8979 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.339 AC: 51495 AN: 151940 Hom.: 8996 Cov.: 31 AF XY: 0.337 AC XY: 25043 AN XY: 74248

African (AFR) AF: 0.348 AC: 14398 AN: 41408

American (AMR) AF: 0.347 AC: 5301 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1953 AN: 3470

East Asian (EAS) AF: 0.422 AC: 2176 AN: 5158

South Asian (SAS) AF: 0.389 AC: 1876 AN: 4818

European-Finnish (FIN) AF: 0.215 AC: 2275 AN: 10564

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22224 AN: 67940

Other (OTH) AF: 0.392 AC: 823 AN: 2102

Alfa AF: 0.326 Hom.: 27097

Bravo AF: 0.351

Asia WGS AF: 0.381 AC: 1326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.56
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs2524123; hg19: chr6-31265314;