rs246992

Variant names:

• chr5-1377448-G-A
• rs246992
• ENST00000504989.1:n.506+2114C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-1377448-G-A
• chr5-1377448-G-T

Variant summary

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

The ENST00000504989.1(LINC01511):​n.506+2114C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,240 control chromosomes in the GnomAD database, including 43,512 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 (43512 hom., cov: 35)
• Consequence: LINC01511 ENST00000504989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504989.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01511	NR_125810.1		n.512+2114C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01511	ENST00000504989.1	TSL:1	n.506+2114C>T		intron	N/A
	LINC01511	ENST00000523692.1	TSL:3	n.384+2217C>T		intron	N/A
	LINC01511	ENST00000653645.1		n.436+2114C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114770 AN: 152122 Hom.: 43477 Cov.: 35

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.754 AC: 114856 AN: 152240 Hom.: 43512 Cov.: 35 AF XY: 0.757 AC XY: 56347 AN XY: 74426

African (AFR) AF: 0.820 AC: 34079 AN: 41552

American (AMR) AF: 0.741 AC: 11338 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2506 AN: 3472

East Asian (EAS) AF: 0.753 AC: 3907 AN: 5186

South Asian (SAS) AF: 0.662 AC: 3189 AN: 4818

European-Finnish (FIN) AF: 0.793 AC: 8405 AN: 10596

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.722 AC: 49105 AN: 68006

Other (OTH) AF: 0.745 AC: 1574 AN: 2112

Alfa AF: 0.750 Hom.: 6770

Bravo AF: 0.755

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.46
PhyloP100		-1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs246992;

hg19: chr5-1377563;