rs9468933

Variant names:

• chr6-31297280-T-A
• rs9468933
• XR_926691.3:n.2357A>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_926691.3(LOC112267902):​n.2357A>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 0.155 in 152,242 control chromosomes in the GnomAD database, including 1,981 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 0.15 (1981 hom., cov: 32)
• Consequence: LOC112267902 XR_926691.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 9 publications found

Genes affected

LOC112267902 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267902	XR_926691.3	n.2357A>T		non_coding_transcript_exon_variant	Exon 5 of 5
LINC02571	NR_149115.1	n.167-2267A>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1	n.172-2267A>T		intron_variant	Intron 1 of 3	4
ENSG00000298396	ENST00000755297.1	n.32+26174T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23515 AN: 152124 Hom.: 1978 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.155 AC: 23528 AN: 152242 Hom.: 1981 Cov.: 32 AF XY: 0.155 AC XY: 11534 AN XY: 74434

African (AFR) AF: 0.176 AC: 7326 AN: 41534

American (AMR) AF: 0.133 AC: 2037 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1204 AN: 3468

East Asian (EAS) AF: 0.101 AC: 523 AN: 5182

South Asian (SAS) AF: 0.181 AC: 875 AN: 4826

European-Finnish (FIN) AF: 0.105 AC: 1111 AN: 10602

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9798 AN: 68012

Other (OTH) AF: 0.174 AC: 368 AN: 2116

Alfa AF: 0.156 Hom.: 262

Bravo AF: 0.157

Asia WGS AF: 0.134 AC: 466 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	6.8
DANN	Benign	0.92
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs9468933; hg19: chr6-31265057;