rs1495186

Variant names:

• chr15-38699255-G-A
• rs1495186
• ENST00000643127.1:n.1260G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-38699255-G-A
• chr15-38699255-G-C
• chr15-38699255-G-T

Variant summary

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

The ENST00000643127.1(LINC02694):​n.1260G>A 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 0.163 in 152,124 control chromosomes in the GnomAD database, including 2,455 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 (2455 hom., cov: 32)
  • Exomes 𝑓: 0.19 (0 hom.)
• Consequence: LINC02694 ENST00000643127.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809
• Publications: 6 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 = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02694	NR_160786.1	n.1260G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02694	ENST00000643127.1	n.1260G>A		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02694	ENST00000644461.1	n.96+71100G>A		intron_variant	Intron 1 of 4
LINC02694	ENST00000645994.2	n.255+2516G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24874 AN: 151974 Hom.: 2455 Cov.: 32

Gnomad AFR AF: 0.0589

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0957

Gnomad SAS AF: 0.0579

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.190

GnomAD4 exome AF: 0.188 AC: 6 AN: 32 Hom.: 0 Cov.: 0 AF XY: 0.182 AC XY: 4 AN XY: 22

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.179 AC: 5 AN: 28

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.163 AC: 24863 AN: 152092 Hom.: 2455 Cov.: 32 AF XY: 0.163 AC XY: 12119 AN XY: 74356

African (AFR) AF: 0.0586 AC: 2435 AN: 41530

American (AMR) AF: 0.209 AC: 3197 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 668 AN: 3468

East Asian (EAS) AF: 0.0952 AC: 492 AN: 5170

South Asian (SAS) AF: 0.0581 AC: 280 AN: 4816

European-Finnish (FIN) AF: 0.232 AC: 2454 AN: 10564

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14708 AN: 67960

Other (OTH) AF: 0.189 AC: 397 AN: 2106

Alfa AF: 0.194 Hom.: 8786

Bravo AF: 0.161

Asia WGS AF: 0.0900 AC: 315 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	3.3
DANN	Benign	0.35
PhyloP100		0.81
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1495186; hg19: chr15-38991456;