rs11579490

Variant names:

• chr1-221877125-C-A
• rs11579490
• ENST00000715677.1:n.635-36672G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-221877125-C-A
• chr1-221877125-C-T

Variant summary

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

The ENST00000715677.1(LINC01705):​n.635-36672G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,070 control chromosomes in the GnomAD database, including 9,318 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 0.34 (9318 hom., cov: 31)
• Consequence: LINC01705 ENST00000715677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 8 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.373 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	ENST00000715677.1		n.635-36672G>T		intron	N/A
	LINC01705	ENST00000826165.1		n.477-36672G>T		intron	N/A
	LINC01705	ENST00000826167.1		n.469+36637G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51585 AN: 151948 Hom.: 9322 Cov.: 31

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.339 AC: 51607 AN: 152070 Hom.: 9318 Cov.: 31 AF XY: 0.335 AC XY: 24875 AN XY: 74320

African (AFR) AF: 0.340 AC: 14095 AN: 41478

American (AMR) AF: 0.262 AC: 4011 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1246 AN: 3464

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5178

South Asian (SAS) AF: 0.287 AC: 1382 AN: 4816

European-Finnish (FIN) AF: 0.382 AC: 4040 AN: 10576

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25602 AN: 67960

Other (OTH) AF: 0.345 AC: 729 AN: 2112

Alfa AF: 0.334 Hom.: 4027

Bravo AF: 0.326

Asia WGS AF: 0.128 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.30
PhyloP100		-0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11579490;

hg19: chr1-222050467;

COSMIC: COSV70858917;