rs246995

Variant names:

• chr5-1374597-G-A
• rs246995
• ENST00000504989.1:n.506+4965C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-1374597-G-A
• chr5-1374597-G-C

Variant summary

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

The ENST00000504989.1(LINC01511):​n.506+4965C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,102 control chromosomes in the GnomAD database, including 42,372 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 0.75 (42372 hom., cov: 32)
• Consequence: LINC01511 ENST00000504989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 4 publications found

Genes affected

LINC01511 (HGNC:51200): (long intergenic non-protein coding RNA 1511)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01511	NR_125810.1	n.512+4965C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01511	ENST00000504989.1	n.506+4965C>T		intron_variant	Intron 1 of 1	1
LINC01511	ENST00000523692.1	n.384+5068C>T		intron_variant	Intron 1 of 1	3
LINC01511	ENST00000653645.1	n.436+4965C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113292 AN: 151984 Hom.: 42338 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.745 AC: 113374 AN: 152102 Hom.: 42372 Cov.: 32 AF XY: 0.749 AC XY: 55668 AN XY: 74362

African (AFR) AF: 0.780 AC: 32352 AN: 41482

American (AMR) AF: 0.737 AC: 11257 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2510 AN: 3472

East Asian (EAS) AF: 0.752 AC: 3885 AN: 5166

South Asian (SAS) AF: 0.663 AC: 3199 AN: 4826

European-Finnish (FIN) AF: 0.803 AC: 8500 AN: 10580

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.726 AC: 49370 AN: 67984

Other (OTH) AF: 0.737 AC: 1556 AN: 2112

Alfa AF: 0.725 Hom.: 26942

Bravo AF: 0.744

Asia WGS AF: 0.727 AC: 2526 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	0.81
DANN	Benign	0.25
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs246995; hg19: chr5-1374712;