1-43945917-A-G

Variant names:

• chr1-43945917-A-G
• rs4448553
• ENST00000784654.1:n.56T>C

Variant summary

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

The ENST00000784654.1(LINC02918):​n.56T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 152,068 control chromosomes in the GnomAD database, including 33,163 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 0.63 (33163 hom., cov: 32)
• Consequence: LINC02918 ENST00000784654.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 20 publications found

Genes affected

LINC02918 (HGNC:55649): (long intergenic non-protein coding RNA 2918)

LOC101929609 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929609	NR_188534.1	n.356+327T>C		intron_variant	Intron 1 of 1
LOC101929609	NR_188535.1	n.119+564T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02918	ENST00000784654.1	n.56T>C		non_coding_transcript_exon_variant	Exon 1 of 2
LINC02918	ENST00000412378.1	n.71+564T>C		intron_variant	Intron 1 of 1	5
LINC02918	ENST00000445226.1	n.43+327T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96019 AN: 151950 Hom.: 33163 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.632 AC: 96040 AN: 152068 Hom.: 33163 Cov.: 32 AF XY: 0.627 AC XY: 46656 AN XY: 74356

African (AFR) AF: 0.344 AC: 14268 AN: 41432

American (AMR) AF: 0.627 AC: 9586 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2360 AN: 3472

East Asian (EAS) AF: 0.626 AC: 3232 AN: 5162

South Asian (SAS) AF: 0.609 AC: 2933 AN: 4816

European-Finnish (FIN) AF: 0.742 AC: 7860 AN: 10590

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53435 AN: 67982

Other (OTH) AF: 0.666 AC: 1407 AN: 2112

Alfa AF: 0.727 Hom.: 52650

Bravo AF: 0.612

Asia WGS AF: 0.609 AC: 2120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.83
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs4448553; hg19: chr1-44411589;