rs11630802

Variant names:

• chr15-81948683-G-A
• rs11630802
• ENST00000559299.2:n.526+4620C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-81948683-G-A
• chr15-81948683-G-C

Variant summary

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

The ENST00000559299.2(LINC01418):​n.526+4620C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,160 control chromosomes in the GnomAD database, including 12,867 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 0.40 (12867 hom., cov: 33)
• Consequence: LINC01418 ENST00000559299.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.634
• Publications: 3 publications found

Genes affected

LINC01418 (HGNC:50711): (long intergenic non-protein coding RNA 1418)

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 (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559299.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01418	ENST00000559299.2	TSL:4	n.526+4620C>T		intron	N/A
	LINC01418	ENST00000657769.1		n.1181+4620C>T		intron	N/A
	LINC01418	ENST00000829414.1		n.756+4620C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61174 AN: 152040 Hom.: 12869 Cov.: 33

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.402 AC: 61198 AN: 152160 Hom.: 12867 Cov.: 33 AF XY: 0.402 AC XY: 29906 AN XY: 74392

African (AFR) AF: 0.333 AC: 13833 AN: 41508

American (AMR) AF: 0.303 AC: 4633 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3468

East Asian (EAS) AF: 0.312 AC: 1616 AN: 5176

South Asian (SAS) AF: 0.285 AC: 1376 AN: 4826

European-Finnish (FIN) AF: 0.542 AC: 5733 AN: 10580

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.461 AC: 31327 AN: 67988

Other (OTH) AF: 0.381 AC: 803 AN: 2108

Alfa AF: 0.335 Hom.: 2371

Bravo AF: 0.381

Asia WGS AF: 0.271 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.33
PhyloP100		0.63

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: rs11630802;

hg19: chr15-82241024;