1-221899656-A-G

Variant names:

• chr1-221899656-A-G
• rs4846734
• ENST00000433576.6:n.482+14106T>C

Variant summary

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

The ENST00000715677.1(LINC01705):​n.634+18936T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,188 control chromosomes in the GnomAD database, including 3,796 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 (3796 hom., cov: 32)
• Consequence: LINC01705 ENST00000715677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715677.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01705	ENST00000433576.6	TSL:5	n.482+14106T>C		intron	N/A
	LINC01705	ENST00000715677.1		n.634+18936T>C		intron	N/A
	LINC01705	ENST00000826165.1		n.476+18936T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33002 AN: 152070 Hom.: 3798 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.217 AC: 33012 AN: 152188 Hom.: 3796 Cov.: 32 AF XY: 0.215 AC XY: 16030 AN XY: 74416

African (AFR) AF: 0.152 AC: 6324 AN: 41540

American (AMR) AF: 0.271 AC: 4142 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 980 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1846 AN: 5186

South Asian (SAS) AF: 0.146 AC: 702 AN: 4824

European-Finnish (FIN) AF: 0.238 AC: 2515 AN: 10570

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

European-Non Finnish (NFE) AF: 0.233 AC: 15829 AN: 67986

Other (OTH) AF: 0.217 AC: 458 AN: 2114

Alfa AF: 0.228 Hom.: 8207

Bravo AF: 0.222

Asia WGS AF: 0.233 AC: 810 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.67
DANN	Benign	0.43
PhyloP100		-0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4846734;

hg19: chr1-222072998;