chr1-185583216-G-A

Position:

• chr1-185583216-G-A

Variant summary

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

The NR_110793.1(LINC01350):​n.147-19888C>T 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 0.151 in 152,116 control chromosomes in the GnomAD database, including 2,179 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 0.15 (2179 hom., cov: 32)
• Consequence: LINC01350 NR_110793.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

LINC01350 (HGNC:50575): (long intergenic non-protein coding RNA 1350)

LOC107985239 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01350	NR_110793.1	n.147-19888C>T		intron_variant, non_coding_transcript_variant
LOC107985239	XR_001738340.2	n.1067-96233G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01350	ENST00000655976.1	n.603-19888C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23036 AN: 151998 Hom.: 2178 Cov.: 32

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0829

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.151 AC: 23032 AN: 152116 Hom.: 2179 Cov.: 32 AF XY: 0.154 AC XY: 11462 AN XY: 74346

Gnomad4 AFR AF: 0.0376

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0828

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.159

Alfa AF: 0.191 Hom.: 1418

Bravo AF: 0.138

Asia WGS AF: 0.114 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12090554; hg19: chr1-185552348;