rs4406273

Variant names:

• chr6-31298313-G-A
• rs4406273
• XR_926691.3:n.1324C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-31298313-G-A
• chr6-31298313-G-T

Variant summary

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

The XR_926691.3(LOC112267902):​n.1324C>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 0.0861 in 152,196 control chromosomes in the GnomAD database, including 594 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 0.086 (594 hom., cov: 32)
• Consequence: LOC112267902 XR_926691.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 42 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 (SAS) allele frequency at 95% confidence interval = 0.0972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267902	XR_926691.3	n.1324C>T		non_coding_transcript_exon_variant	Exon 5 of 5
LINC02571	NR_149115.1	n.166+3159C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1	n.171+3159C>T		intron_variant	Intron 1 of 3	4
ENSG00000298396	ENST00000755297.1	n.32+27207G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0861 AC: 13096 AN: 152078 Hom.: 592 Cov.: 32

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0418

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0606

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0916

Gnomad OTH AF: 0.0900

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

GnomAD4 genome AF: 0.0861 AC: 13100 AN: 152196 Hom.: 594 Cov.: 32 AF XY: 0.0857 AC XY: 6374 AN XY: 74406

African (AFR) AF: 0.0909 AC: 3776 AN: 41536

American (AMR) AF: 0.0638 AC: 976 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3468

East Asian (EAS) AF: 0.0419 AC: 217 AN: 5180

South Asian (SAS) AF: 0.105 AC: 504 AN: 4812

European-Finnish (FIN) AF: 0.0606 AC: 642 AN: 10596

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0916 AC: 6230 AN: 68000

Other (OTH) AF: 0.0876 AC: 185 AN: 2112

Alfa AF: 0.0822 Hom.: 1000

Bravo AF: 0.0865

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.43
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs4406273; hg19: chr6-31266090; COSMIC: COSV73434407;