chr1-221872104-G-T

Variant names:

• chr1-221872104-G-T
• rs6691170
• ENST00000715677.1:n.635-31651C>A

Variant summary

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

The ENST00000715677.1(LINC01705):​n.635-31651C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,088 control chromosomes in the GnomAD database, including 8,981 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 0.33 (8981 hom., cov: 33)
• Consequence: LINC01705 ENST00000715677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 93 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 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.635-31651C>A		intron	N/A
	LINC01705	ENST00000826165.1		n.477-31651C>A		intron	N/A
	LINC01705	ENST00000826167.1		n.470-31651C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50661 AN: 151970 Hom.: 8985 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.333 AC: 50683 AN: 152088 Hom.: 8981 Cov.: 33 AF XY: 0.329 AC XY: 24495 AN XY: 74370

African (AFR) AF: 0.338 AC: 14036 AN: 41470

American (AMR) AF: 0.262 AC: 4001 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1239 AN: 3468

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5182

South Asian (SAS) AF: 0.280 AC: 1351 AN: 4822

European-Finnish (FIN) AF: 0.377 AC: 3980 AN: 10568

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

European-Non Finnish (NFE) AF: 0.365 AC: 24848 AN: 67986

Other (OTH) AF: 0.344 AC: 726 AN: 2112

Alfa AF: 0.353 Hom.: 22701

Bravo AF: 0.321

Asia WGS AF: 0.127 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.66
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6691170; hg19: chr1-222045446; COSMIC: COSV52393577;