rs1433887

Positions:

• chr15-38936902-T-C

Variant summary

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

The ENST00000560484.1(ENSG00000259345):​n.254+37253A>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 0.432 in 152,070 control chromosomes in the GnomAD database, including 14,863 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 0.43 (14863 hom., cov: 33)
• Consequence: ENST00000560484.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370777	XR_007064587.1	n.1527-28642A>G		intron_variant, non_coding_transcript_variant
LOC105370777	XR_007064588.1	n.705-28642A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000560484.1	n.254+37253A>G		intron_variant, non_coding_transcript_variant		4
LINC02694	ENST00000644461.1	n.158+113843T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65619 AN: 151950 Hom.: 14827 Cov.: 33

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.432 AC: 65707 AN: 152070 Hom.: 14863 Cov.: 33 AF XY: 0.427 AC XY: 31743 AN XY: 74340

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.387

Alfa AF: 0.419 Hom.: 1706

Bravo AF: 0.437

Asia WGS AF: 0.287 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.3
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1433887; hg19: chr15-39229103;