rs11811613

Variant names:

• chr1-221882061-A-G
• rs11811613
• ENST00000433576.6:n.572-777T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-221882061-A-G
• chr1-221882061-A-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+36531T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,108 control chromosomes in the GnomAD database, including 5,210 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 0.24 (5210 hom., cov: 32)
• Consequence: LINC01705 ENST00000715677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 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.572-777T>C		intron	N/A
	LINC01705	ENST00000715677.1		n.634+36531T>C		intron	N/A
	LINC01705	ENST00000826165.1		n.476+36531T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36219 AN: 151990 Hom.: 5210 Cov.: 32

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.238 AC: 36222 AN: 152108 Hom.: 5210 Cov.: 32 AF XY: 0.242 AC XY: 17991 AN XY: 74324

African (AFR) AF: 0.0881 AC: 3660 AN: 41522

American (AMR) AF: 0.344 AC: 5254 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3468

East Asian (EAS) AF: 0.426 AC: 2201 AN: 5172

South Asian (SAS) AF: 0.152 AC: 733 AN: 4822

European-Finnish (FIN) AF: 0.347 AC: 3663 AN: 10546

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18669 AN: 67982

Other (OTH) AF: 0.254 AC: 536 AN: 2112

Alfa AF: 0.264 Hom.: 17870

Bravo AF: 0.238

Asia WGS AF: 0.273 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.35
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs11811613; hg19: chr1-222055403;