chr18-64119804-A-T

Variant names:

• chr18-64119804-A-T
• rs2850711
• ENST00000323355.3:n.257-21164T>A

Variant summary

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

The ENST00000323355.3(LINC00305):​n.257-21164T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 151,988 control chromosomes in the GnomAD database, including 1,533 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 0.14 (1533 hom., cov: 31)
• Consequence: LINC00305 ENST00000323355.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.794
• Publications: 10 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00305	NR_027245.2	n.315-21164T>A		intron_variant	Intron 1 of 3
LINC01924	NR_033881.1	n.146-7581A>T		intron_variant	Intron 1 of 9
LINC00305	NR_190189.1	n.220-7994T>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00305	ENST00000323355.3	n.257-21164T>A		intron_variant	Intron 1 of 3	1
LINC01924	ENST00000589376.1	n.146-7581A>T		intron_variant	Intron 1 of 9	1
LINC01924	ENST00000649298.1	n.889-7581A>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21425 AN: 151870 Hom.: 1533 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0956

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.141 AC: 21433 AN: 151988 Hom.: 1533 Cov.: 31 AF XY: 0.139 AC XY: 10294 AN XY: 74284

African (AFR) AF: 0.127 AC: 5258 AN: 41470

American (AMR) AF: 0.0954 AC: 1455 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 355 AN: 3466

East Asian (EAS) AF: 0.141 AC: 730 AN: 5176

South Asian (SAS) AF: 0.0999 AC: 479 AN: 4794

European-Finnish (FIN) AF: 0.166 AC: 1757 AN: 10590

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10933 AN: 67932

Other (OTH) AF: 0.138 AC: 290 AN: 2108

Alfa AF: 0.155 Hom.: 232

Bravo AF: 0.137

Asia WGS AF: 0.103 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.6
DANN	Benign	0.70
PhyloP100		0.79
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: rs2850711; hg19: chr18-61787038;