rs4489979

Variant names:

• chr15-38755238-T-C
• rs4489979
• ENST00000831954.1:n.515A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-38755238-T-C
• chr15-38755238-T-G

Variant summary

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

The ENST00000831954.1(ENSG00000308144):​n.515A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,060 control chromosomes in the GnomAD database, including 24,886 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 0.51 (24886 hom., cov: 32)
• Consequence: ENSG00000308144 ENST00000831954.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769
• Publications: 2 publications found

Genes affected

ENSG00000308144 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724253	XR_007064585.1	n.426A>G		non_coding_transcript_exon_variant	Exon 5 of 5
LOC102724253	XR_429514.4	n.320A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LOC102724253	XR_932122.3	n.475A>G		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308144	ENST00000831954.1	n.515A>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000308144	ENST00000831955.1	n.466A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02694	ENST00000644461.1	n.97-67760T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78146 AN: 151942 Hom.: 24890 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.514 AC: 78141 AN: 152060 Hom.: 24886 Cov.: 32 AF XY: 0.513 AC XY: 38159 AN XY: 74318

African (AFR) AF: 0.137 AC: 5706 AN: 41502

American (AMR) AF: 0.613 AC: 9369 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2647 AN: 3468

East Asian (EAS) AF: 0.429 AC: 2214 AN: 5162

South Asian (SAS) AF: 0.326 AC: 1571 AN: 4816

European-Finnish (FIN) AF: 0.675 AC: 7113 AN: 10538

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47501 AN: 67968

Other (OTH) AF: 0.579 AC: 1223 AN: 2112

Alfa AF: 0.434 Hom.: 5304

Bravo AF: 0.500

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.65
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs4489979; hg19: chr15-39047439;