rs7555040

Variant names:

• chr1-47403644-A-G
• rs7555040
• ENST00000420876.1:n.158+4676T>C

Variant summary

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

The ENST00000420876.1(LINC01389):​n.158+4676T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,154 control chromosomes in the GnomAD database, including 1,095 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 0.11 (1095 hom., cov: 32)
• Consequence: LINC01389 ENST00000420876.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 6 publications found

Genes affected

LINC01389 (HGNC:50661): (long intergenic non-protein coding RNA 1389)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420876.1. 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
	LINC01389	NR_126355.1		n.404+4676T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01389	ENST00000420876.1	TSL:3	n.158+4676T>C		intron	N/A
	LINC01389	ENST00000828805.1		n.208-22501T>C		intron	N/A
	LINC01389	ENST00000828806.1		n.92+13587T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16554 AN: 152036 Hom.: 1094 Cov.: 32

Gnomad AFR AF: 0.0289

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0992

Gnomad SAS AF: 0.0500

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.109 AC: 16554 AN: 152154 Hom.: 1095 Cov.: 32 AF XY: 0.107 AC XY: 7981 AN XY: 74394

African (AFR) AF: 0.0288 AC: 1198 AN: 41528

American (AMR) AF: 0.122 AC: 1859 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 576 AN: 3470

East Asian (EAS) AF: 0.0988 AC: 512 AN: 5180

South Asian (SAS) AF: 0.0496 AC: 239 AN: 4820

European-Finnish (FIN) AF: 0.141 AC: 1491 AN: 10606

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10158 AN: 67956

Other (OTH) AF: 0.159 AC: 337 AN: 2114

Alfa AF: 0.130 Hom.: 3004

Bravo AF: 0.106

Asia WGS AF: 0.0700 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	8.6
DANN	Benign	0.92
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs7555040; hg19: chr1-47869316;