ENST00000412445.1:n.165-8894C>T

Variant names:

• chr1-221927606-G-A
• rs12743521
• ENST00000412445.1:n.165-8894C>T

Variant summary

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

The ENST00000412445.1(LINC01705):​n.165-8894C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,040 control chromosomes in the GnomAD database, including 4,217 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 0.22 (4217 hom., cov: 31)
• Consequence: LINC01705 ENST00000412445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684
• Publications: 2 publications found

Genes affected

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

LINC02257 (HGNC:53159): (long intergenic non-protein coding RNA 2257)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412445.1. 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
	LINC02257	NR_149057.1		n.162-8894C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01705	ENST00000412445.1	TSL:2	n.165-8894C>T		intron	N/A
	LINC01705	ENST00000433576.6	TSL:5	n.156-8894C>T		intron	N/A
	LINC01705	ENST00000715677.1		n.514-8894C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33863 AN: 151922 Hom.: 4209 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.223 AC: 33888 AN: 152040 Hom.: 4217 Cov.: 31 AF XY: 0.223 AC XY: 16596 AN XY: 74334

African (AFR) AF: 0.113 AC: 4691 AN: 41508

American (AMR) AF: 0.268 AC: 4094 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1555 AN: 5138

South Asian (SAS) AF: 0.220 AC: 1059 AN: 4816

European-Finnish (FIN) AF: 0.252 AC: 2665 AN: 10580

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18113 AN: 67944

Other (OTH) AF: 0.232 AC: 490 AN: 2108

Alfa AF: 0.241 Hom.: 3321

Bravo AF: 0.220

Asia WGS AF: 0.286 AC: 995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.10
DANN	Benign	0.35
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs12743521; hg19: chr1-222100948;