chr15-38711562-C-T

Variant names:

• chr15-38711562-C-T
• rs2643217
• ENST00000644461.1:n.96+83407C>T

Variant summary

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

The ENST00000644461.1(LINC02694):​n.96+83407C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,116 control chromosomes in the GnomAD database, including 2,355 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 0.16 (2355 hom., cov: 32)
• Consequence: LINC02694 ENST00000644461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 8 publications found

Genes affected

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644461.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02694	ENST00000644461.1		n.96+83407C>T		intron	N/A
	LINC02694	ENST00000645416.2		n.52+8638C>T		intron	N/A
	LINC02694	ENST00000645994.2		n.255+14823C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23598 AN: 151998 Hom.: 2356 Cov.: 32

Gnomad AFR AF: 0.0460

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.0389

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.155 AC: 23587 AN: 152116 Hom.: 2355 Cov.: 32 AF XY: 0.153 AC XY: 11384 AN XY: 74364

African (AFR) AF: 0.0459 AC: 1905 AN: 41532

American (AMR) AF: 0.175 AC: 2676 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 744 AN: 3470

East Asian (EAS) AF: 0.0388 AC: 201 AN: 5180

South Asian (SAS) AF: 0.0550 AC: 265 AN: 4818

European-Finnish (FIN) AF: 0.219 AC: 2312 AN: 10570

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14856 AN: 67968

Other (OTH) AF: 0.188 AC: 397 AN: 2114

Alfa AF: 0.186 Hom.: 4393

Bravo AF: 0.150

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.40
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2643217; hg19: chr15-39003763;