1-221830566-C-T

Variant names:

• chr1-221830566-C-T
• rs4846728
• ENST00000665303.2:n.375-2810G>A

Variant summary

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

The ENST00000665303.2(LINC01705):​n.375-2810G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,228 control chromosomes in the GnomAD database, including 4,734 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 0.23 (4734 hom., cov: 33)
• Consequence: LINC01705 ENST00000665303.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 3 publications found

Genes affected

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

LINC01655 (HGNC:52443): (long intergenic non-protein coding RNA 1655)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01655	NR_125989.1	n.333-2810G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01705	ENST00000665303.2	n.375-2810G>A		intron_variant	Intron 3 of 4
LINC01705	ENST00000826175.1	n.432+3726G>A		intron_variant	Intron 3 of 5
LINC01705	ENST00000826176.1	n.374-2810G>A		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34481 AN: 152110 Hom.: 4729 Cov.: 33

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.227 AC: 34491 AN: 152228 Hom.: 4734 Cov.: 33 AF XY: 0.229 AC XY: 17043 AN XY: 74432

African (AFR) AF: 0.0819 AC: 3404 AN: 41572

American (AMR) AF: 0.202 AC: 3094 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3470

East Asian (EAS) AF: 0.493 AC: 2549 AN: 5168

South Asian (SAS) AF: 0.316 AC: 1526 AN: 4824

European-Finnish (FIN) AF: 0.280 AC: 2961 AN: 10584

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

European-Non Finnish (NFE) AF: 0.285 AC: 19376 AN: 68002

Other (OTH) AF: 0.207 AC: 437 AN: 2110

Alfa AF: 0.250 Hom.: 1250

Bravo AF: 0.213

Asia WGS AF: 0.312 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.40
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs4846728; hg19: chr1-222003908;