rs16899202

Variant names:

• chr6-31298522-G-C
• rs16899202
• XR_926691.3:n.1115C>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.1115C>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 0.00813 in 151,332 control chromosomes in the GnomAD database, including 53 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 0.0081 (53 hom., cov: 31)
• Consequence: LOC112267902 XR_926691.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.102 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.166+2950C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02571	ENST00000539514.1	TSL:4	n.171+2950C>G		intron	N/A
	ENSG00000298396	ENST00000755297.1		n.32+27416G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00811 AC: 1227 AN: 151218 Hom.: 53 Cov.: 31

Gnomad AFR AF: 0.00116

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0165

Gnomad ASJ AF: 0.00665

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0613

Gnomad FIN AF: 0.00219

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000339

Gnomad OTH AF: 0.00626

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

GnomAD4 genome AF: 0.00813 AC: 1230 AN: 151332 Hom.: 53 Cov.: 31 AF XY: 0.00983 AC XY: 726 AN XY: 73878

African (AFR) AF: 0.00116 AC: 48 AN: 41466

American (AMR) AF: 0.0166 AC: 248 AN: 14956

Ashkenazi Jewish (ASJ) AF: 0.00665 AC: 23 AN: 3458

East Asian (EAS) AF: 0.109 AC: 560 AN: 5118

South Asian (SAS) AF: 0.0611 AC: 288 AN: 4710

European-Finnish (FIN) AF: 0.00219 AC: 23 AN: 10504

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.000339 AC: 23 AN: 67820

Other (OTH) AF: 0.00810 AC: 17 AN: 2100

Alfa AF: 0.00279 Hom.: 0

Bravo AF: 0.00873

Asia WGS AF: 0.0960 AC: 334 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.2
DANN	Benign	0.73
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs16899202; hg19: chr6-31266299;