rs10847023

Variant names:

• chr12-125959974-T-C
• rs10847023
• ENST00000502479.1:n.4722-1022A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000502479.1(LINC00939):​n.4722-1022A>G variant causes a intron 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 ENST00000502479.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.847
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502479.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00939	NR_034132.1		n.1814-1022A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00939	ENST00000502479.1	TSL:1	n.4722-1022A>G		intron	N/A
	LINC00939	ENST00000545784.7	TSL:1	n.1833-1022A>G		intron	N/A
	LINC00939	ENST00000507313.6	TSL:2	n.2615-1022A>G		intron	N/A

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

African (AFR) AF: 0.122 AC: 5085 AN: 41532

American (AMR) AF: 0.324 AC: 4953 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3470

East Asian (EAS) AF: 0.0322 AC: 167 AN: 5182

South Asian (SAS) AF: 0.125 AC: 604 AN: 4828

European-Finnish (FIN) AF: 0.152 AC: 1609 AN: 10602

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10784 AN: 68008

Other (OTH) AF: 0.178 AC: 376 AN: 2110

Alfa AF: 0.162 Hom.: 6592

Bravo AF: 0.172

Asia WGS AF: 0.0950 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.69
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs10847023; hg19: chr12-126444520;