rs16899202

Variant names:

• chr6-31298522-G-C
• rs16899202
• XR_926691.3:n.1115C>G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267902	XR_926691.3	n.1115C>G		non_coding_transcript_exon_variant	Exon 5 of 5
LINC02571	NR_149115.1	n.166+2950C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1	n.171+2950C>G		intron_variant	Intron 1 of 3	4

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

Gnomad4 AFR AF: 0.00116

Gnomad4 AMR AF: 0.0166

Gnomad4 ASJ AF: 0.00665

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0611

Gnomad4 FIN AF: 0.00219

Gnomad4 NFE AF: 0.000339

Gnomad4 OTH AF: 0.00810

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16899202; hg19: chr6-31266299;