rs12726661

Variant names:

• chr1-221894446-A-G
• rs12726661
• ENST00000433576.6:n.483-10558T>C

Variant summary

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

The ENST00000433576.6(LINC01705):​n.483-10558T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 145,922 control chromosomes in the GnomAD database, including 5,404 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 0.27 (5404 hom., cov: 32)
• Consequence: LINC01705 ENST00000433576.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345
• Publications: 1 publications found

Genes affected

LINC01705 (HGNC:52493): (long intergenic non-protein coding RNA 1705)

ENSG00000307440 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433576.6. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01705	ENST00000433576.6	TSL:5	n.483-10558T>C		intron	N/A
	LINC01705	ENST00000715677.1		n.634+24146T>C		intron	N/A
	LINC01705	ENST00000826165.1		n.476+24146T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.268 AC: 39054 AN: 145812 Hom.: 5402 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.00147

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.268 AC: 39062 AN: 145922 Hom.: 5404 Cov.: 32 AF XY: 0.266 AC XY: 18952 AN XY: 71294

African (AFR) AF: 0.252 AC: 9842 AN: 39090

American (AMR) AF: 0.211 AC: 3094 AN: 14652

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 829 AN: 3388

East Asian (EAS) AF: 0.00147 AC: 7 AN: 4764

South Asian (SAS) AF: 0.229 AC: 1003 AN: 4374

European-Finnish (FIN) AF: 0.340 AC: 3530 AN: 10372

Middle Eastern (MID) AF: 0.250 AC: 70 AN: 280

European-Non Finnish (NFE) AF: 0.299 AC: 19749 AN: 66082

Other (OTH) AF: 0.279 AC: 565 AN: 2026

Alfa AF: 0.188 Hom.: 662

Asia WGS AF: 0.0950 AC: 333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.7
DANN	Benign	0.83
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs12726661; hg19: chr1-222067788;