1-221887680-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 ENST00000715677.1(LINC01705):​n.634+30912C>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 ENST00000715677.1 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.

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	ENST00000433576.6	TSL:5	n.483-3792C>T		intron	N/A
	LINC01705	ENST00000715677.1		n.634+30912C>T		intron	N/A
	LINC01705	ENST00000826165.1		n.476+30912C>T		intron	N/A

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 v4.9

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;