chr6-31297713-T-C

Variant names:

• chr6-31297713-T-C
• rs2247056
• XR_926691.3:n.1924A>G

Variant summary

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

The XR_926691.3(LOC112267902):​n.1924A>G 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 0.804 in 152,104 control chromosomes in the GnomAD database, including 49,582 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 0.80 (49582 hom., cov: 31)
• Consequence: LOC112267902 XR_926691.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 112 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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267902	XR_926691.3	n.1924A>G		non_coding_transcript_exon_variant	Exon 5 of 5
LINC02571	NR_149115.1	n.167-2700A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1	n.172-2700A>G		intron_variant	Intron 1 of 3	4
ENSG00000298396	ENST00000755297.1	n.32+26607T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122155 AN: 151986 Hom.: 49526 Cov.: 31

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.804 AC: 122262 AN: 152104 Hom.: 49582 Cov.: 31 AF XY: 0.809 AC XY: 60136 AN XY: 74340

African (AFR) AF: 0.876 AC: 36353 AN: 41514

American (AMR) AF: 0.848 AC: 12949 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3230 AN: 3472

East Asian (EAS) AF: 0.839 AC: 4335 AN: 5166

South Asian (SAS) AF: 0.881 AC: 4246 AN: 4820

European-Finnish (FIN) AF: 0.775 AC: 8191 AN: 10572

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50241 AN: 67974

Other (OTH) AF: 0.855 AC: 1798 AN: 2104

Alfa AF: 0.763 Hom.: 190963

Bravo AF: 0.813

Asia WGS AF: 0.883 AC: 3072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.9
DANN	Benign	0.18
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs2247056; hg19: chr6-31265490;