rs3906272

Variant names:

• chr6-31295147-C-T
• rs3906272
• ENST00000539514.1:n.172-134G>A

Variant summary

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

The ENST00000539514.1(LINC02571):​n.172-134G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,008 control chromosomes in the GnomAD database, including 1,932 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 0.15 (1932 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC02571 ENST00000539514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02571	NR_149115.1	n.167-134G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1	n.172-134G>A		intron_variant	Intron 1 of 3	4
ENSG00000298396	ENST00000755297.1	n.32+24041C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23384 AN: 151890 Hom.: 1929 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.175

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

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: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.154 AC: 23397 AN: 152008 Hom.: 1932 Cov.: 32 AF XY: 0.154 AC XY: 11468 AN XY: 74340

African (AFR) AF: 0.175 AC: 7250 AN: 41418

American (AMR) AF: 0.132 AC: 2022 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1199 AN: 3462

East Asian (EAS) AF: 0.102 AC: 526 AN: 5178

South Asian (SAS) AF: 0.182 AC: 875 AN: 4812

European-Finnish (FIN) AF: 0.105 AC: 1108 AN: 10594

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9767 AN: 67956

Other (OTH) AF: 0.173 AC: 366 AN: 2112

Alfa AF: 0.124 Hom.: 476

Bravo AF: 0.157

Asia WGS AF: 0.130 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.8
DANN	Benign	0.65
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs3906272; hg19: chr6-31262924;