rs7171171

Variant names:

• chr15-38614840-A-G
• rs7171171
• ENST00000791581.1:n.448+2385A>G

Variant summary

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

The ENST00000791581.1(LINC02694):​n.448+2385A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,200 control chromosomes in the GnomAD database, including 4,620 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 0.23 (4620 hom., cov: 33)
• Consequence: LINC02694 ENST00000791581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362
• Publications: 35 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02694	ENST00000791581.1	n.448+2385A>G		intron_variant	Intron 3 of 5
LINC02694	ENST00000791582.1	n.448+2385A>G		intron_variant	Intron 3 of 4
LINC02694	ENST00000791584.1	n.443+2385A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34919 AN: 152082 Hom.: 4613 Cov.: 33

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.0449

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.230 AC: 34954 AN: 152200 Hom.: 4620 Cov.: 33 AF XY: 0.225 AC XY: 16719 AN XY: 74412

African (AFR) AF: 0.352 AC: 14629 AN: 41508

American (AMR) AF: 0.157 AC: 2407 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 833 AN: 3470

East Asian (EAS) AF: 0.0450 AC: 233 AN: 5182

South Asian (SAS) AF: 0.0994 AC: 480 AN: 4828

European-Finnish (FIN) AF: 0.209 AC: 2210 AN: 10594

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13407 AN: 67998

Other (OTH) AF: 0.218 AC: 462 AN: 2116

Alfa AF: 0.207 Hom.: 10857

Bravo AF: 0.231

Asia WGS AF: 0.0790 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.47
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs7171171; hg19: chr15-38907041;