rs4778944

Variant names:

• chr15-81911334-T-C
• rs4778944
• XR_001751641.2:n.4579A>G

Variant summary

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

The XR_001751641.2(LINC01418):​n.4579A>G 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 0.417 in 152,038 control chromosomes in the GnomAD database, including 13,518 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 0.42 (13518 hom., cov: 32)
• Consequence: LINC01418 XR_001751641.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 1 publications found

Genes affected

LINC01418 (HGNC:50711): (long intergenic non-protein coding RNA 1418)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01418	XR_001751641.2	n.4579A>G		non_coding_transcript_exon_variant	Exon 5 of 5
LINC01418	XR_001751642.2	n.4461A>G		non_coding_transcript_exon_variant	Exon 4 of 4
LINC01418	XR_932527.3	n.4759A>G		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01418	ENST00000559299.2	n.859+4013A>G		intron_variant	Intron 6 of 7	4
LINC01418	ENST00000829414.1	n.978+14339A>G		intron_variant	Intron 7 of 7
LINC01418	ENST00000829415.1	n.428+14339A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63373 AN: 151920 Hom.: 13499 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.417 AC: 63431 AN: 152038 Hom.: 13518 Cov.: 32 AF XY: 0.422 AC XY: 31343 AN XY: 74330

African (AFR) AF: 0.441 AC: 18274 AN: 41446

American (AMR) AF: 0.332 AC: 5066 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1306 AN: 3470

East Asian (EAS) AF: 0.220 AC: 1137 AN: 5176

South Asian (SAS) AF: 0.554 AC: 2671 AN: 4822

European-Finnish (FIN) AF: 0.478 AC: 5052 AN: 10576

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28453 AN: 67958

Other (OTH) AF: 0.420 AC: 885 AN: 2106

Alfa AF: 0.415 Hom.: 22218

Bravo AF: 0.403

Asia WGS AF: 0.399 AC: 1389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	8.3
DANN	Benign	0.85
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4778944; hg19: chr15-82203675;