rs6695584

Variant names:

• chr1-221988647-A-G
• rs6695584
• ENST00000715677.1:n.355-10129T>C

Variant summary

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

The ENST00000715677.1(LINC01705):​n.355-10129T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,186 control chromosomes in the GnomAD database, including 2,955 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 0.19 (2955 hom., cov: 32)
• Consequence: LINC01705 ENST00000715677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 16 publications found

Genes affected

LINC01705 (HGNC:52493): (long intergenic non-protein coding RNA 1705)

ENSG00000307458 (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 (AMR) allele frequency at 95% confidence interval = 0.222 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01705	ENST00000715677.1		n.355-10129T>C		intron	N/A
	LINC01705	ENST00000826165.1		n.355+69767T>C		intron	N/A
	LINC01705	ENST00000826166.1		n.265+69767T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28989 AN: 152068 Hom.: 2957 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.190 AC: 28984 AN: 152186 Hom.: 2955 Cov.: 32 AF XY: 0.194 AC XY: 14409 AN XY: 74410

African (AFR) AF: 0.147 AC: 6111 AN: 41534

American (AMR) AF: 0.228 AC: 3492 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3468

East Asian (EAS) AF: 0.217 AC: 1127 AN: 5182

South Asian (SAS) AF: 0.156 AC: 752 AN: 4820

European-Finnish (FIN) AF: 0.266 AC: 2816 AN: 10592

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13420 AN: 67972

Other (OTH) AF: 0.189 AC: 400 AN: 2114

Alfa AF: 0.196 Hom.: 1897

Bravo AF: 0.186

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.32
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6695584; hg19: chr1-222161989;