rs1424401

Variant names:

• chr18-55973548-G-A
• rs1424401
• ENST00000589440.1:n.406-44180G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-55973548-G-A
• chr18-55973548-G-C

Variant summary

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

The ENST00000589440.1(LINC01905):​n.406-44180G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,844 control chromosomes in the GnomAD database, including 27,075 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 0.58 (27075 hom., cov: 31)
• Consequence: LINC01905 ENST00000589440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 1 publications found

Genes affected

LINC01905 (HGNC:52724): (long intergenic non-protein coding RNA 1905)

LINC01416 (HGNC:51645): (long intergenic non-protein coding RNA 1416)

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 = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01905	ENST00000589440.1	n.406-44180G>A		intron_variant	Intron 1 of 2	2
LINC01416	ENST00000654280.1	n.1512+23160C>T		intron_variant	Intron 1 of 3
LINC01416	ENST00000655696.1	n.1303+23160C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88686 AN: 151726 Hom.: 27043 Cov.: 31

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.585 AC: 88772 AN: 151844 Hom.: 27075 Cov.: 31 AF XY: 0.583 AC XY: 43283 AN XY: 74188

African (AFR) AF: 0.399 AC: 16506 AN: 41336

American (AMR) AF: 0.652 AC: 9961 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2432 AN: 3468

East Asian (EAS) AF: 0.472 AC: 2432 AN: 5150

South Asian (SAS) AF: 0.627 AC: 3018 AN: 4814

European-Finnish (FIN) AF: 0.610 AC: 6423 AN: 10536

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45875 AN: 67956

Other (OTH) AF: 0.617 AC: 1305 AN: 2114

Alfa AF: 0.647 Hom.: 129843

Bravo AF: 0.573

Asia WGS AF: 0.541 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.31
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs1424401; hg19: chr18-53640779;