rs6687758

Variant names:

• chr1-221991606-A-G
• rs6687758
• ENST00000715677.1:n.355-13088T>C

Variant summary

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

The ENST00000715677.1(LINC01705):​n.355-13088T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,140 control chromosomes in the GnomAD database, including 3,261 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 0.20 (3261 hom., cov: 32)
• Consequence: LINC01705 ENST00000715677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 122 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01705	ENST00000715677.1	n.355-13088T>C		intron_variant	Intron 2 of 4
LINC01705	ENST00000826165.1	n.355+66808T>C		intron_variant	Intron 2 of 3
LINC01705	ENST00000826166.1	n.265+66808T>C		intron_variant	Intron 1 of 2
ENSG00000307458	ENST00000826417.1	n.97+14888A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30757 AN: 152020 Hom.: 3263 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.202 AC: 30755 AN: 152140 Hom.: 3261 Cov.: 32 AF XY: 0.205 AC XY: 15245 AN XY: 74370

African (AFR) AF: 0.188 AC: 7784 AN: 41494

American (AMR) AF: 0.233 AC: 3553 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3466

East Asian (EAS) AF: 0.217 AC: 1121 AN: 5174

South Asian (SAS) AF: 0.156 AC: 750 AN: 4822

European-Finnish (FIN) AF: 0.266 AC: 2819 AN: 10588

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13450 AN: 67998

Other (OTH) AF: 0.195 AC: 411 AN: 2112

Alfa AF: 0.197 Hom.: 13922

Bravo AF: 0.200

Asia WGS AF: 0.153 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.85
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs6687758; hg19: chr1-222164948; COSMIC: COSV52393599;