1-221896824-C-T

Variant names:

• chr1-221896824-C-T
• rs12738322
• ENST00000433576.6:n.483-12936G>A

Variant summary

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

The ENST00000433576.6(LINC01705):​n.483-12936G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 151,928 control chromosomes in the GnomAD database, including 5,424 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 0.26 (5424 hom., cov: 33)
• Consequence: LINC01705 ENST00000433576.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 1 publications found

Genes affected

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

ENSG00000307440 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433576.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01705	ENST00000433576.6	TSL:5	n.483-12936G>A		intron	N/A
	LINC01705	ENST00000715677.1		n.634+21768G>A		intron	N/A
	LINC01705	ENST00000826165.1		n.476+21768G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39087 AN: 151810 Hom.: 5421 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.257 AC: 39097 AN: 151928 Hom.: 5424 Cov.: 33 AF XY: 0.256 AC XY: 18984 AN XY: 74232

African (AFR) AF: 0.237 AC: 9844 AN: 41452

American (AMR) AF: 0.202 AC: 3090 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 832 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5184

South Asian (SAS) AF: 0.209 AC: 1005 AN: 4816

European-Finnish (FIN) AF: 0.339 AC: 3562 AN: 10522

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19745 AN: 67906

Other (OTH) AF: 0.268 AC: 568 AN: 2116

Alfa AF: 0.227 Hom.: 949

Bravo AF: 0.244

Asia WGS AF: 0.0950 AC: 331 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	1.4
DANN	Benign	0.49
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs12738322; hg19: chr1-222070166;