rs2894207

Variant names:

• chr6-31295974-T-C
• rs2894207
• ENST00000539514.1:n.172-961A>G

Variant summary

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

The ENST00000539514.1(LINC02571):​n.172-961A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 151,902 control chromosomes in the GnomAD database, including 3,447 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 0.21 (3447 hom., cov: 32)
• Consequence: LINC02571 ENST00000539514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 62 publications found

Genes affected

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

ENSG00000298396 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02571	NR_149115.1	n.167-961A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1	n.172-961A>G		intron_variant	Intron 1 of 3	4
ENSG00000298396	ENST00000755297.1	n.32+24868T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31334 AN: 151784 Hom.: 3440 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.206 AC: 31354 AN: 151902 Hom.: 3447 Cov.: 32 AF XY: 0.210 AC XY: 15627 AN XY: 74244

African (AFR) AF: 0.205 AC: 8478 AN: 41430

American (AMR) AF: 0.253 AC: 3863 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1315 AN: 3464

East Asian (EAS) AF: 0.180 AC: 931 AN: 5168

South Asian (SAS) AF: 0.303 AC: 1458 AN: 4806

European-Finnish (FIN) AF: 0.170 AC: 1789 AN: 10552

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12718 AN: 67918

Other (OTH) AF: 0.223 AC: 469 AN: 2102

Alfa AF: 0.186 Hom.: 5474

Bravo AF: 0.211

Asia WGS AF: 0.270 AC: 936 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.50
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2894207; hg19: chr6-31263751;