chr18-64349268-C-T

Variant names:

• chr18-64349268-C-T
• rs7229505
• ENST00000589376.1:n.580+55153C>T

Variant summary

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

The ENST00000589376.1(LINC01924):​n.580+55153C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,004 control chromosomes in the GnomAD database, including 2,382 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 0.13 (2382 hom., cov: 32)
• Consequence: LINC01924 ENST00000589376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 0 publications found

Genes affected

LINC01924 (HGNC:27600): (long intergenic non-protein coding RNA 1924)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01924	NR_033881.1	n.580+55153C>T		intron_variant	Intron 5 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01924	ENST00000589376.1	n.580+55153C>T		intron_variant	Intron 5 of 9	1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19773 AN: 151888 Hom.: 2380 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0315

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0457

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.130 AC: 19808 AN: 152004 Hom.: 2382 Cov.: 32 AF XY: 0.129 AC XY: 9568 AN XY: 74302

African (AFR) AF: 0.317 AC: 13126 AN: 41408

American (AMR) AF: 0.112 AC: 1708 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0315 AC: 109 AN: 3464

East Asian (EAS) AF: 0.125 AC: 647 AN: 5158

South Asian (SAS) AF: 0.123 AC: 593 AN: 4810

European-Finnish (FIN) AF: 0.0248 AC: 263 AN: 10584

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0457 AC: 3105 AN: 67998

Other (OTH) AF: 0.102 AC: 215 AN: 2104

Alfa AF: 0.0916 Hom.: 170

Bravo AF: 0.144

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.29
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7229505; hg19: chr18-62016503;