rs10847023

Positions:

• chr12-125959974-T-C

Variant summary

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

The NR_034132.1(LINC00939):​n.1814-1022A>G 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 0.159 in 152,224 control chromosomes in the GnomAD database, including 2,351 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 0.16 (2351 hom., cov: 33)
• Consequence: LINC00939 NR_034132.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.847

Genes affected

LINC00939 (HGNC:48631): (long intergenic non-protein coding RNA 939)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00939	NR_034132.1	n.1814-1022A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00939	ENST00000502479.1	n.4722-1022A>G		intron_variant, non_coding_transcript_variant		1
LINC00939	ENST00000507313.6	n.2615-1022A>G		intron_variant, non_coding_transcript_variant		2
LINC00939	ENST00000545784.7	n.1833-1022A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24179 AN: 152106 Hom.: 2346 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0323

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.159 AC: 24216 AN: 152224 Hom.: 2351 Cov.: 33 AF XY: 0.161 AC XY: 11949 AN XY: 74432

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0322

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.178

Alfa AF: 0.164 Hom.: 3197

Bravo AF: 0.172

Asia WGS AF: 0.0950 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10847023; hg19: chr12-126444520;