rs11163687

Variant names:

• chr1-83199436-A-G
• rs11163687
• ENST00000715939.1:n.271+32570T>C

Variant summary

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

The ENST00000715939.1(LINC01725):​n.271+32570T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.097 in 152,238 control chromosomes in the GnomAD database, including 913 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 0.097 (913 hom., cov: 32)
• Consequence: LINC01725 ENST00000715939.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 5 publications found

Genes affected

LINC01725 (HGNC:52513): (long intergenic non-protein coding RNA 1725)

ENSG00000310120 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715939.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01725	ENST00000715939.1		n.271+32570T>C		intron	N/A
	LINC01725	ENST00000715967.1		n.593+32570T>C		intron	N/A
	LINC01725	ENST00000715968.1		n.259+32570T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0971 AC: 14765 AN: 152120 Hom.: 911 Cov.: 32

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.0575

Gnomad SAS AF: 0.0999

Gnomad FIN AF: 0.0845

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0970 AC: 14768 AN: 152238 Hom.: 913 Cov.: 32 AF XY: 0.0948 AC XY: 7055 AN XY: 74448

African (AFR) AF: 0.0263 AC: 1093 AN: 41580

American (AMR) AF: 0.160 AC: 2447 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3470

East Asian (EAS) AF: 0.0579 AC: 300 AN: 5184

South Asian (SAS) AF: 0.0998 AC: 481 AN: 4822

European-Finnish (FIN) AF: 0.0845 AC: 897 AN: 10620

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8892 AN: 67974

Other (OTH) AF: 0.0919 AC: 194 AN: 2112

Alfa AF: 0.116 Hom.: 444

Bravo AF: 0.101

Asia WGS AF: 0.0880 AC: 305 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.6
DANN	Benign	0.87
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs11163687; hg19: chr1-83665119;