rs2850711

chr18-64119804-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027245.1(LINC00305):n.253-21164T>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 0.141 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 NR_027245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.794

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 -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/exons	MANE	UniProt
LINC00305	NR_027245.1	n.253-21164T>A		intron_variant, non_coding_transcript_variant
LINC01924	NR_033881.1	n.146-7581A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01924	ENST00000589376.1	n.146-7581A>T		intron_variant, non_coding_transcript_variant		1
LINC00305	ENST00000666468.1	n.315-21164T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0954

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0999

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.138

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2850711; hg19: chr18-61787038;