rs12144971

Variant names:

• chr1-221859143-C-T
• rs12144971
• ENST00000715677.1:n.635-18690G>A

Variant summary

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

The ENST00000715677.1(LINC01705):​n.635-18690G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,072 control chromosomes in the GnomAD database, including 22,083 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 0.53 (22083 hom., cov: 32)
• Consequence: LINC01705 ENST00000715677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 3 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715677.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01705	ENST00000715677.1		n.635-18690G>A		intron	N/A
	LINC01705	ENST00000826165.1		n.477-18690G>A		intron	N/A
	LINC01705	ENST00000826167.1		n.470-18690G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81116 AN: 151954 Hom.: 22060 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.534 AC: 81191 AN: 152072 Hom.: 22083 Cov.: 32 AF XY: 0.531 AC XY: 39451 AN XY: 74322

African (AFR) AF: 0.499 AC: 20700 AN: 41446

American (AMR) AF: 0.427 AC: 6525 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1690 AN: 3470

East Asian (EAS) AF: 0.399 AC: 2062 AN: 5168

South Asian (SAS) AF: 0.538 AC: 2590 AN: 4818

European-Finnish (FIN) AF: 0.571 AC: 6030 AN: 10568

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39758 AN: 67990

Other (OTH) AF: 0.527 AC: 1111 AN: 2110

Alfa AF: 0.562 Hom.: 92307

Bravo AF: 0.517

Asia WGS AF: 0.430 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.9
DANN	Benign	0.56
PhyloP100		-0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12144971;

hg19: chr1-222032485;

COSMIC: COSV60032674;