ENST00000412445.1:n.165-10308G>A

Variant names:

• chr1-221929020-C-T
• rs7544501
• ENST00000412445.1:n.165-10308G>A

Variant summary

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

The ENST00000412445.1(LINC01705):​n.165-10308G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,966 control chromosomes in the GnomAD database, including 4,570 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 0.24 (4570 hom., cov: 31)
• Consequence: LINC01705 ENST00000412445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02257	NR_149057.1	n.162-10308G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01705	ENST00000412445.1	n.165-10308G>A		intron_variant	Intron 1 of 3	2
LINC01705	ENST00000433576.6	n.156-10308G>A		intron_variant	Intron 1 of 5	5
LINC01705	ENST00000715677.1	n.514-10308G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36032 AN: 151848 Hom.: 4560 Cov.: 31

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.237 AC: 36063 AN: 151966 Hom.: 4570 Cov.: 31 AF XY: 0.238 AC XY: 17647 AN XY: 74266

African (AFR) AF: 0.151 AC: 6263 AN: 41466

American (AMR) AF: 0.282 AC: 4300 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 991 AN: 3462

East Asian (EAS) AF: 0.338 AC: 1736 AN: 5140

South Asian (SAS) AF: 0.225 AC: 1082 AN: 4814

European-Finnish (FIN) AF: 0.252 AC: 2660 AN: 10572

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18268 AN: 67926

Other (OTH) AF: 0.243 AC: 512 AN: 2106

Alfa AF: 0.259 Hom.: 7791

Bravo AF: 0.236

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.73
DANN	Benign	0.48
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7544501; hg19: chr1-222102362;