rs1541918

Variant names:

• chr5-172544483-C-A
• rs1541918
• ENST00000652199.1:n.434-121G>T

Variant summary

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

The ENST00000652199.1(LINC01944):​n.434-121G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,226 control chromosomes in the GnomAD database, including 979 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 (979 hom., cov: 32)
• Consequence: LINC01944 ENST00000652199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 4 publications found

Genes affected

LINC01944 (HGNC:52768): (long intergenic non-protein coding RNA 1944)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.133 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
LINC01944	ENST00000652199.1	n.434-121G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17118 AN: 152108 Hom.: 976 Cov.: 32

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0732

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.113 AC: 17127 AN: 152226 Hom.: 979 Cov.: 32 AF XY: 0.112 AC XY: 8335 AN XY: 74454

African (AFR) AF: 0.0942 AC: 3913 AN: 41520

American (AMR) AF: 0.124 AC: 1898 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3470

East Asian (EAS) AF: 0.103 AC: 533 AN: 5190

South Asian (SAS) AF: 0.141 AC: 682 AN: 4820

European-Finnish (FIN) AF: 0.0732 AC: 777 AN: 10610

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.124 AC: 8434 AN: 68008

Other (OTH) AF: 0.129 AC: 273 AN: 2114

Alfa AF: 0.117 Hom.: 2037

Bravo AF: 0.112

Asia WGS AF: 0.125 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.5
DANN	Benign	0.75
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs1541918; hg19: chr5-171971486;