chr6-31296615-G-A

Variant names:

• chr6-31296615-G-A
• rs9380237
• ENST00000539514.1:n.172-1602C>T

Variant summary

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

The ENST00000539514.1(LINC02571):​n.172-1602C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,824 control chromosomes in the GnomAD database, including 7,372 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 0.30 (7372 hom., cov: 31)
• Consequence: LINC02571 ENST00000539514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 8 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02571	NR_149115.1	n.167-1602C>T		intron_variant	Intron 1 of 3
LOC112267902	XR_926691.3	n.*211C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1	n.172-1602C>T		intron_variant	Intron 1 of 3	4
ENSG00000298396	ENST00000755297.1	n.32+25509G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46112 AN: 151706 Hom.: 7352 Cov.: 31

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.304 AC: 46161 AN: 151824 Hom.: 7372 Cov.: 31 AF XY: 0.312 AC XY: 23141 AN XY: 74180

African (AFR) AF: 0.304 AC: 12562 AN: 41390

American (AMR) AF: 0.365 AC: 5574 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1561 AN: 3460

East Asian (EAS) AF: 0.410 AC: 2119 AN: 5174

South Asian (SAS) AF: 0.453 AC: 2184 AN: 4820

European-Finnish (FIN) AF: 0.265 AC: 2783 AN: 10498

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18273 AN: 67916

Other (OTH) AF: 0.341 AC: 718 AN: 2108

Alfa AF: 0.279 Hom.: 4532

Bravo AF: 0.310

Asia WGS AF: 0.434 AC: 1505 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.30
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs9380237; hg19: chr6-31264392;