rs710059

Positions:

• chr14-61639547-C-T

Variant summary

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

The NR_039985.1(LINC03033):​n.222-11415C>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 0.605 in 152,054 control chromosomes in the GnomAD database, including 33,410 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 0.60 (33410 hom., cov: 32)
• Consequence: LINC03033 NR_039985.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938

Genes affected

LINC03033 (HGNC:44292): (long intergenic non-protein coding RNA 3033)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03033	NR_039985.1	n.222-11415C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03033	ENST00000229465.10	n.222-11415C>T		intron_variant, non_coding_transcript_variant		2
LINC03033	ENST00000556569.5	n.357-11415C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91945 AN: 151936 Hom.: 33404 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.605 AC: 91966 AN: 152054 Hom.: 33410 Cov.: 32 AF XY: 0.615 AC XY: 45755 AN XY: 74348

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.715

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.614

Alfa AF: 0.681 Hom.: 4854

Bravo AF: 0.571

Asia WGS AF: 0.730 AC: 2539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs710059; hg19: chr14-62106265;