chr1-221887680-G-A

Variant names:

• chr1-221887680-G-A
• rs11118883
• ENST00000433576.6:n.483-3792C>T

Variant summary

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

The ENST00000433576.6(LINC01705):​n.483-3792C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 151,788 control chromosomes in the GnomAD database, including 5,982 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 (5982 hom., cov: 32)
• Consequence: LINC01705 ENST00000433576.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 12 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904517	XR_007066885.1	n.331-28398G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01705	ENST00000433576.6	n.483-3792C>T		intron_variant	Intron 4 of 5	5
LINC01705	ENST00000715677.1	n.634+30912C>T		intron_variant	Intron 4 of 4
LINC01705	ENST00000826165.1	n.476+30912C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40989 AN: 151670 Hom.: 5980 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.270 AC: 40995 AN: 151788 Hom.: 5982 Cov.: 32 AF XY: 0.268 AC XY: 19864 AN XY: 74164

African (AFR) AF: 0.242 AC: 10013 AN: 41348

American (AMR) AF: 0.212 AC: 3231 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 990 AN: 3462

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5190

South Asian (SAS) AF: 0.225 AC: 1076 AN: 4790

European-Finnish (FIN) AF: 0.346 AC: 3639 AN: 10520

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20993 AN: 67896

Other (OTH) AF: 0.280 AC: 592 AN: 2112

Alfa AF: 0.286 Hom.: 17516

Bravo AF: 0.256

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.57
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs11118883; hg19: chr1-222061022;