rs17120400

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-60225916-G-A
• chr1-60225916-G-T

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;