rs641025

Variant names:

• chr3-152182436-C-G
• rs641025
• ENST00000689682.2:n.174-7563G>C

Variant summary

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

The ENST00000689682.2(LINC02917):​n.174-7563G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 151,944 control chromosomes in the GnomAD database, including 35,914 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 0.68 (35914 hom., cov: 31)
• Consequence: LINC02917 ENST00000689682.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 3 publications found

Genes affected

LINC02917 (HGNC:55643): (long intergenic non-protein coding RNA 2917)

LOC101928166 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928166	NR_136178.1	n.58-7563G>C		intron_variant	Intron 1 of 2
LINC02917	NR_186000.1	n.55+22937G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02917	ENST00000689682.2	n.174-7563G>C		intron_variant	Intron 1 of 2
LINC02917	ENST00000781727.1	n.256-7563G>C		intron_variant	Intron 1 of 2
LINC02917	ENST00000781728.1	n.91+22937G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.685 AC: 103941 AN: 151826 Hom.: 35890 Cov.: 31

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.685 AC: 104026 AN: 151944 Hom.: 35914 Cov.: 31 AF XY: 0.687 AC XY: 51043 AN XY: 74276

African (AFR) AF: 0.772 AC: 32028 AN: 41468

American (AMR) AF: 0.680 AC: 10359 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2480 AN: 3468

East Asian (EAS) AF: 0.714 AC: 3685 AN: 5162

South Asian (SAS) AF: 0.766 AC: 3687 AN: 4816

European-Finnish (FIN) AF: 0.631 AC: 6656 AN: 10546

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.632 AC: 42960 AN: 67932

Other (OTH) AF: 0.673 AC: 1422 AN: 2112

Alfa AF: 0.656 Hom.: 4130

Bravo AF: 0.689

Asia WGS AF: 0.754 AC: 2623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.61
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs641025; hg19: chr3-151900225;