rs4924304

Variant names:

• chr15-38807647-G-A
• rs4924304
• ENST00000644461.1:n.97-15351G>A

Variant summary

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

The ENST00000644461.1(LINC02694):​n.97-15351G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0426 in 152,210 control chromosomes in the GnomAD database, including 585 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 0.043 (585 hom., cov: 32)
• Consequence: LINC02694 ENST00000644461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630

Genes affected

LINC02694 (HGNC:33796): (long intergenic non-protein coding RNA 2694)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 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
LINC02694	ENST00000644461.1	n.97-15351G>A		intron_variant	Intron 1 of 4
LINC02694	ENST00000645416.2	n.227-15351G>A		intron_variant	Intron 2 of 2
LINC02694	ENST00000646232.1	n.164-15351G>A		intron_variant	Intron 2 of 3
LINC02694	ENST00000647456.1	n.658+74326G>A		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.0425 AC: 6469 AN: 152092 Hom.: 586 Cov.: 32

Gnomad AFR AF: 0.0106

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0291

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0426 AC: 6481 AN: 152210 Hom.: 585 Cov.: 32 AF XY: 0.0473 AC XY: 3520 AN XY: 74430

Gnomad4 AFR AF: 0.0105

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.00663

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0291

Gnomad4 NFE AF: 0.0178

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0320 Hom.: 543

Bravo AF: 0.0477

Asia WGS AF: 0.249 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4924304; hg19: chr15-39099848;