rs315791

Variant names:

• chr5-170308916-A-C
• rs315791
• ENST00000511921.2:n.2057T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-170308916-A-C
• chr5-170308916-A-T

Variant summary

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

The ENST00000511921.2(ENSG00000250274):​n.2057T>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 0.471 in 152,036 control chromosomes in the GnomAD database, including 16,998 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 0.47 (16998 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000250274 ENST00000511921.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253
• Publications: 16 publications found

Genes affected

ENSG00000250274 (HGNC:):

LINC01366 (HGNC:27416): (long intergenic non-protein coding RNA 1366)

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 = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100128059	NR_147701.1	n.1967T>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250274	ENST00000511921.2	n.2057T>G		non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC01366	ENST00000653905.1	n.84+1111A>C		intron_variant	Intron 1 of 3
LINC01366	ENST00000770366.1	n.226+1461A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71554 AN: 151918 Hom.: 16981 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.489

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 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: 0.471 AC: 71601 AN: 152036 Hom.: 16998 Cov.: 32 AF XY: 0.469 AC XY: 34831 AN XY: 74302

African (AFR) AF: 0.419 AC: 17346 AN: 41446

American (AMR) AF: 0.509 AC: 7771 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1753 AN: 3472

East Asian (EAS) AF: 0.525 AC: 2720 AN: 5178

South Asian (SAS) AF: 0.402 AC: 1932 AN: 4810

European-Finnish (FIN) AF: 0.410 AC: 4330 AN: 10554

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.503 AC: 34173 AN: 67990

Other (OTH) AF: 0.497 AC: 1047 AN: 2108

Alfa AF: 0.493 Hom.: 58972

Bravo AF: 0.478

Asia WGS AF: 0.470 AC: 1633 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	2.8
DANN	Benign	0.49
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs315791; hg19: chr5-169735920;