rs472975

Positions:

• chr1-185565344-A-G

Variant summary

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

The NR_110793.1(LINC01350):​n.147-2016T>C 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 0.44 in 152,028 control chromosomes in the GnomAD database, including 15,677 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 0.44 (15677 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01350 NR_110793.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01350	NR_110793.1	n.147-2016T>C		intron_variant, non_coding_transcript_variant
LOC107985239	XR_001738340.2	n.1066+86266A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01350	ENST00000655976.1	n.603-2016T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66837 AN: 151912 Hom.: 15661 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.440 AC: 66890 AN: 152028 Hom.: 15677 Cov.: 32 AF XY: 0.442 AC XY: 32849 AN XY: 74310

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.418

Alfa AF: 0.430 Hom.: 1797

Bravo AF: 0.429

Asia WGS AF: 0.331 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.29
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs472975; hg19: chr1-185534476;