4-112007545-A-G

Variant names:

• chr4-112007545-A-G
• rs6848323
• ENST00000508010.2:n.194+12869T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000508010.2(LINC02945):​n.194+12869T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,014 control chromosomes in the GnomAD database, including 26,013 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 0.56 (26013 hom., cov: 32)
• Consequence: LINC02945 ENST00000508010.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659
• Publications: 2 publications found

Genes affected

LINC02945 (HGNC:55960): (long intergenic non-protein coding RNA 2945)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02945	NR_186680.1	n.98+65020T>C		intron_variant	Intron 1 of 2
LINC02945	NR_186681.1	n.184+12869T>C		intron_variant	Intron 2 of 3
LINC02945	NR_186682.1	n.82+104644T>C		intron_variant	Intron 1 of 2
LINC02945	NR_186683.1	n.62+65056T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02945	ENST00000508010.2	n.194+12869T>C		intron_variant	Intron 2 of 4	5
LINC02945	ENST00000511219.1	n.134+65020T>C		intron_variant	Intron 1 of 2	3
LINC02945	ENST00000679735.2	n.187+12869T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85153 AN: 151894 Hom.: 25973 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.561 AC: 85248 AN: 152014 Hom.: 26013 Cov.: 32 AF XY: 0.561 AC XY: 41659 AN XY: 74282

African (AFR) AF: 0.794 AC: 32960 AN: 41508

American (AMR) AF: 0.605 AC: 9242 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1922 AN: 3470

East Asian (EAS) AF: 0.809 AC: 4180 AN: 5170

South Asian (SAS) AF: 0.463 AC: 2225 AN: 4802

European-Finnish (FIN) AF: 0.417 AC: 4391 AN: 10542

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28678 AN: 67934

Other (OTH) AF: 0.554 AC: 1166 AN: 2104

Alfa AF: 0.361 Hom.: 1050

Bravo AF: 0.593

Asia WGS AF: 0.615 AC: 2132 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	14
DANN	Benign	0.49
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs6848323; hg19: chr4-112928701;