rs3905495

Variant names:

• chr6-31297762-G-A
• rs3905495
• XR_926691.3:n.1875C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-31297762-G-A
• chr6-31297762-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.1875C>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 0.394 in 151,982 control chromosomes in the GnomAD database, including 12,060 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 0.39 (12060 hom., cov: 32)
• Consequence: LOC112267902 XR_926691.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 32 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.459 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.167-2749C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02571	ENST00000539514.1	TSL:4	n.172-2749C>T		intron	N/A
	ENSG00000298396	ENST00000755297.1		n.32+26656G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59817 AN: 151862 Hom.: 12044 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.394 AC: 59866 AN: 151982 Hom.: 12060 Cov.: 32 AF XY: 0.401 AC XY: 29775 AN XY: 74270

African (AFR) AF: 0.440 AC: 18229 AN: 41438

American (AMR) AF: 0.451 AC: 6894 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1153 AN: 3472

East Asian (EAS) AF: 0.411 AC: 2123 AN: 5164

South Asian (SAS) AF: 0.475 AC: 2291 AN: 4822

European-Finnish (FIN) AF: 0.460 AC: 4851 AN: 10544

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23085 AN: 67964

Other (OTH) AF: 0.393 AC: 826 AN: 2100

Alfa AF: 0.361 Hom.: 37759

Bravo AF: 0.393

Asia WGS AF: 0.485 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.4
DANN	Benign	0.24
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs3905495; hg19: chr6-31265539;