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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904517	XR_007066885.1	n.330+13648C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01705	ENST00000715677.1	n.635-25260G>A		intron_variant	Intron 4 of 4
LINC01705	ENST00000826165.1	n.477-25260G>A		intron_variant	Intron 3 of 3
LINC01705	ENST00000826167.1	n.470-25260G>A		intron_variant	Intron 4 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs4240931; hg19: chr1-222039055;