15-39023157-G-C

Position:

• chr15-39023157-G-C

Variant summary

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

The ENST00000560484.1(ENSG00000259345):​n.173+48346C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,090 control chromosomes in the GnomAD database, including 7,671 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 0.30 (7671 hom., cov: 32)
• Consequence: ENST00000560484.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

(HGNC:):

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370781	XR_002957707.2	n.90-1056G>C		intron_variant, non_coding_transcript_variant
LOC105370777	XR_007064586.1	n.1445+48346C>G		intron_variant, non_coding_transcript_variant
LOC105370777	XR_007064587.1	n.1445+48346C>G		intron_variant, non_coding_transcript_variant
LOC105370777	XR_007064588.1	n.623+48346C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000560484.1	n.173+48346C>G		intron_variant, non_coding_transcript_variant		4
LINC02694	ENST00000644461.1	n.159-149822G>C		intron_variant, non_coding_transcript_variant
	ENST00000657583.1	n.133-1056G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45926 AN: 151972 Hom.: 7669 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.302 AC: 45934 AN: 152090 Hom.: 7671 Cov.: 32 AF XY: 0.301 AC XY: 22377 AN XY: 74376

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.322

Alfa AF: 0.221 Hom.: 522

Bravo AF: 0.296

Asia WGS AF: 0.341 AC: 1184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12907914; hg19: chr15-39315358;