rs4529739

Positions:

• chr1-60239111-T-C

Variant summary

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

The XR_947430.2(LINC02778):​n.150-3714T>C 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 0.0692 in 152,220 control chromosomes in the GnomAD database, including 510 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 0.069 (510 hom., cov: 32)
• Consequence: LINC02778 XR_947430.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548

Genes affected

LINC02778 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02778	XR_947430.2	n.150-3714T>C		intron_variant, non_coding_transcript_variant
LOC105378761	XR_947431.2	n.617+12476A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10536 AN: 152102 Hom.: 510 Cov.: 32

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0450

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0886

Gnomad FIN AF: 0.0778

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0692 AC: 10539 AN: 152220 Hom.: 510 Cov.: 32 AF XY: 0.0676 AC XY: 5030 AN XY: 74424

Gnomad4 AFR AF: 0.0187

Gnomad4 AMR AF: 0.0580

Gnomad4 ASJ AF: 0.0450

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0893

Gnomad4 FIN AF: 0.0778

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0700

Alfa AF: 0.0959 Hom.: 438

Bravo AF: 0.0647

Asia WGS AF: 0.0280 AC: 101 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4529739; hg19: chr1-60704783;