XR_947430.2:n.150-16909G>A

Variant names:

• chr1-60225916-G-A
• rs17120400
• XR_947430.2:n.150-16909G>A

Variant summary

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

The XR_947430.2(LINC02778):​n.150-16909G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,712 control chromosomes in the GnomAD database, including 1,854 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 0.15 (1854 hom., cov: 31)
• Consequence: LINC02778 XR_947430.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• Publications: 1 publications found

Genes affected

LINC02778 (HGNC:54298): (long intergenic non-protein coding RNA 2778)

LOC105378761 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02778	XR_947430.2	n.150-16909G>A		intron_variant	Intron 1 of 4
LOC105378761	XR_947431.2	n.617+25671C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22797 AN: 151592 Hom.: 1856 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.150 AC: 22814 AN: 151712 Hom.: 1854 Cov.: 31 AF XY: 0.153 AC XY: 11317 AN XY: 74124

African (AFR) AF: 0.210 AC: 8673 AN: 41344

American (AMR) AF: 0.196 AC: 2981 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3468

East Asian (EAS) AF: 0.188 AC: 956 AN: 5086

South Asian (SAS) AF: 0.120 AC: 577 AN: 4802

European-Finnish (FIN) AF: 0.174 AC: 1826 AN: 10508

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6943 AN: 67942

Other (OTH) AF: 0.136 AC: 287 AN: 2112

Alfa AF: 0.119 Hom.: 5290

Bravo AF: 0.160

Asia WGS AF: 0.174 AC: 605 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	0.42
DANN	Benign	0.49
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs17120400; hg19: chr1-60691588;