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. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000559299.2(ENSG00000259692):​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: ENSG00000259692 ENST00000559299.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.634

Genes affected

ENSG00000259692 (HGNC:50711): (long intergenic non-protein coding RNA 1418)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01418	XR_001751639.2	n.401+4620C>T		intron_variant	Intron 3 of 6
LINC01418	XR_001751640.2	n.413+4620C>T		intron_variant	Intron 3 of 5
LINC01418	XR_001751641.2	n.115+18385C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259692	ENST00000559299.2	n.526+4620C>T		intron_variant	Intron 3 of 7	4
ENSG00000259692	ENST00000657769.1	n.1181+4620C>T		intron_variant	Intron 6 of 8

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

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.381

Alfa AF: 0.340 Hom.: 1484

Bravo AF: 0.381

Asia WGS AF: 0.271 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11630802; hg19: chr15-82241024;