18-64130436-A-T

Position:

• chr18-64130436-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_027245.1(LINC00305):​n.252+18339T>A variant causes a intron, non coding transcript 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 NR_027245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00305	NR_027245.1	n.252+18339T>A		intron_variant, non_coding_transcript_variant
LINC01924	NR_033881.1	n.200+2997A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01924	ENST00000589376.1	n.200+2997A>T		intron_variant, non_coding_transcript_variant		1
LINC00305	ENST00000666468.1	n.314+18339T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0516

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.222

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1517162; hg19: chr18-61797670;