rs6684428

Variant names:

• chr1-55894140-T-A
• rs6684428
• ENST00000646266.1:n.357+46603T>A

Variant summary

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

The ENST00000646266.1(LINC01755):​n.357+46603T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,212 control chromosomes in the GnomAD database, including 2,277 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 0.17 (2277 hom., cov: 32)
• Consequence: LINC01755 ENST00000646266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 8 publications found

Genes affected

LINC01755 (HGNC:52543): (long intergenic non-protein coding RNA 1755)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 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
LINC01755	ENST00000646266.1	n.357+46603T>A		intron_variant	Intron 3 of 11
LINC01755	ENST00000648749.1	n.2603+22682T>A		intron_variant	Intron 2 of 4
LINC01755	ENST00000661225.1	n.185+46603T>A		intron_variant	Intron 2 of 9

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25564 AN: 152092 Hom.: 2274 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0456

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.168 AC: 25592 AN: 152212 Hom.: 2277 Cov.: 32 AF XY: 0.170 AC XY: 12686 AN XY: 74424

African (AFR) AF: 0.163 AC: 6766 AN: 41532

American (AMR) AF: 0.215 AC: 3286 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3472

East Asian (EAS) AF: 0.0455 AC: 236 AN: 5182

South Asian (SAS) AF: 0.247 AC: 1190 AN: 4824

European-Finnish (FIN) AF: 0.171 AC: 1808 AN: 10602

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10877 AN: 68004

Other (OTH) AF: 0.171 AC: 362 AN: 2112

Alfa AF: 0.164 Hom.: 285

Bravo AF: 0.170

Asia WGS AF: 0.154 AC: 537 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.37
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs6684428; hg19: chr1-56359813;