ENST00000323355.3:n.256+18339T>A

Variant names:

• chr18-64130436-A-T
• rs1517162
• ENST00000323355.3:n.256+18339T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000323355.3(LINC00305):​n.256+18339T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,054 control chromosomes in the GnomAD database, including 4,188 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 0.21 (4188 hom., cov: 32)
• Consequence: LINC00305 ENST00000323355.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68
• Publications: 3 publications found

Genes affected

LINC00305 (HGNC:28597): (long intergenic non-protein coding RNA 305) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00305	NR_027245.2	n.314+18339T>A		intron_variant	Intron 1 of 3
LINC01924	NR_033881.1	n.200+2997A>T		intron_variant	Intron 2 of 9
LINC00305	NR_190189.1	n.219+18339T>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00305	ENST00000323355.3	n.256+18339T>A		intron_variant	Intron 1 of 3	1
LINC01924	ENST00000589376.1	n.200+2997A>T		intron_variant	Intron 2 of 9	1
LINC01924	ENST00000649298.1	n.943+2997A>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31765 AN: 151936 Hom.: 4186 Cov.: 32

Gnomad AFR AF: 0.0518

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.209 AC: 31751 AN: 152054 Hom.: 4188 Cov.: 32 AF XY: 0.211 AC XY: 15662 AN XY: 74334

African (AFR) AF: 0.0516 AC: 2142 AN: 41508

American (AMR) AF: 0.177 AC: 2695 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1123 AN: 3470

East Asian (EAS) AF: 0.328 AC: 1691 AN: 5158

South Asian (SAS) AF: 0.347 AC: 1672 AN: 4824

European-Finnish (FIN) AF: 0.240 AC: 2543 AN: 10574

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18988 AN: 67942

Other (OTH) AF: 0.222 AC: 469 AN: 2112

Alfa AF: 0.230 Hom.: 543

Bravo AF: 0.198

Asia WGS AF: 0.257 AC: 891 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	14
DANN	Benign	0.93
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs1517162; hg19: chr18-61797670;