rs11577023

Variant names:

• chr1-221888631-T-C
• rs11577023
• ENST00000433576.6:n.483-4743A>G

Variant summary

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

The ENST00000433576.6(LINC01705):​n.483-4743A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,200 control chromosomes in the GnomAD database, including 6,142 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 (6142 hom., cov: 33)
• Consequence: LINC01705 ENST00000433576.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904517	XR_007066885.1	n.331-27447T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01705	ENST00000433576.6	n.483-4743A>G		intron_variant	Intron 4 of 5	5
LINC01705	ENST00000715677.1	n.634+29961A>G		intron_variant	Intron 4 of 4
LINC01705	ENST00000826165.1	n.476+29961A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41476 AN: 152082 Hom.: 6142 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.273 AC: 41485 AN: 152200 Hom.: 6142 Cov.: 33 AF XY: 0.270 AC XY: 20123 AN XY: 74432

African (AFR) AF: 0.242 AC: 10037 AN: 41538

American (AMR) AF: 0.224 AC: 3424 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 903 AN: 3466

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5192

South Asian (SAS) AF: 0.224 AC: 1082 AN: 4820

European-Finnish (FIN) AF: 0.342 AC: 3629 AN: 10600

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21320 AN: 67970

Other (OTH) AF: 0.288 AC: 608 AN: 2112

Alfa AF: 0.295 Hom.: 6998

Bravo AF: 0.260

Asia WGS AF: 0.104 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.0070
DANN	Benign	0.34
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11577023; hg19: chr1-222061973;