6-31301531-C-T

Variant names:

• chr6-31301531-C-T
• rs3873385
• ENST00000539514.1:n.112G>A

Variant summary

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

The ENST00000539514.1(LINC02571):​n.112G>A 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 0.141 in 151,988 control chromosomes in the GnomAD database, including 1,764 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 0.14 (1764 hom., cov: 32)
  • Exomes 𝑓: 0.083 (0 hom.)
• Consequence: LINC02571 ENST00000539514.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 23 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02571	NR_149115.1	n.107G>A		non_coding_transcript_exon_variant	Exon 1 of 4
LOC112267902	XR_926691.3	n.1060+228G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1	n.112G>A		non_coding_transcript_exon_variant	Exon 1 of 4	4
ENSG00000298396	ENST00000755297.1	n.32+30425C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21439 AN: 151858 Hom.: 1761 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0739

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.167

GnomAD4 exome AF: 0.0833 AC: 1 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.141 AC: 21450 AN: 151976 Hom.: 1764 Cov.: 32 AF XY: 0.137 AC XY: 10205 AN XY: 74296

African (AFR) AF: 0.109 AC: 4534 AN: 41448

American (AMR) AF: 0.170 AC: 2604 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 619 AN: 3462

East Asian (EAS) AF: 0.313 AC: 1613 AN: 5158

South Asian (SAS) AF: 0.113 AC: 545 AN: 4824

European-Finnish (FIN) AF: 0.0739 AC: 782 AN: 10580

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10248 AN: 67916

Other (OTH) AF: 0.171 AC: 360 AN: 2110

Alfa AF: 0.148 Hom.: 5132

Bravo AF: 0.150

Asia WGS AF: 0.183 AC: 637 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	5.8
DANN	Benign	0.59
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs3873385; hg19: chr6-31269308;