rs4240931

Variant names:

• chr1-221865713-C-T
• rs4240931
• ENST00000715677.1:n.635-25260G>A

Variant summary

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

The ENST00000715677.1(LINC01705):​n.635-25260G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,988 control chromosomes in the GnomAD database, including 16,202 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 0.46 (16202 hom., cov: 32)
• Consequence: LINC01705 ENST00000715677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 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.635-25260G>A		intron	N/A
	LINC01705	ENST00000826165.1		n.477-25260G>A		intron	N/A
	LINC01705	ENST00000826167.1		n.470-25260G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69354 AN: 151870 Hom.: 16201 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.457 AC: 69385 AN: 151988 Hom.: 16202 Cov.: 32 AF XY: 0.461 AC XY: 34237 AN XY: 74296

African (AFR) AF: 0.462 AC: 19163 AN: 41438

American (AMR) AF: 0.572 AC: 8732 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1782 AN: 3472

East Asian (EAS) AF: 0.631 AC: 3265 AN: 5174

South Asian (SAS) AF: 0.466 AC: 2244 AN: 4818

European-Finnish (FIN) AF: 0.430 AC: 4539 AN: 10548

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.415 AC: 28195 AN: 67950

Other (OTH) AF: 0.468 AC: 987 AN: 2108

Alfa AF: 0.438 Hom.: 46946

Bravo AF: 0.472

Asia WGS AF: 0.590 AC: 2050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.73
PhyloP100		-0.48

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: rs4240931;

hg19: chr1-222039055;