rs1519337

Variant names:

• chr4-138011920-G-A
• rs1519337
• ENST00000655176.1:n.661-13314G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-138011920-G-A
• chr4-138011920-G-C
• chr4-138011920-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655176.1(ENSG00000287144):​n.661-13314G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,216 control chromosomes in the GnomAD database, including 60,366 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 0.89 (60366 hom., cov: 32)
• Consequence: ENSG00000287144 ENST00000655176.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.509

Genes affected

ENSG00000287144 (HGNC:):

LINC00616 (HGNC:44065): (long intergenic non-protein coding RNA 616)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287144	ENST00000655176.1	n.661-13314G>A		intron_variant	Intron 3 of 8
LINC00616	ENST00000656980.1	n.844-33155C>T		intron_variant	Intron 6 of 6
LINC00616	ENST00000661963.1	n.806-33155C>T		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135162 AN: 152098 Hom.: 60324 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.964

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.889 AC: 135265 AN: 152216 Hom.: 60366 Cov.: 32 AF XY: 0.890 AC XY: 66224 AN XY: 74438

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.964

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.964

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.907

Alfa AF: 0.912 Hom.: 37506

Bravo AF: 0.876

Asia WGS AF: 0.910 AC: 3157 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.8
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1519337; hg19: chr4-138933074;