XR_930217.2:n.1288-3438C>T

Variant names:

• chr9-107661739-C-T
• rs4979219
• XR_930217.2:n.1288-3438C>T

Variant summary

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

The XR_930217.2(LOC105376205):​n.1288-3438C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,138 control chromosomes in the GnomAD database, including 1,564 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 0.13 (1564 hom., cov: 32)
• Consequence: LOC105376205 XR_930217.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 5 publications found

Genes affected

LOC105376205 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19730 AN: 152018 Hom.: 1561 Cov.: 32

Gnomad AFR AF: 0.0473

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.130 AC: 19734 AN: 152138 Hom.: 1564 Cov.: 32 AF XY: 0.129 AC XY: 9560 AN XY: 74388

African (AFR) AF: 0.0472 AC: 1959 AN: 41508

American (AMR) AF: 0.204 AC: 3113 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3468

East Asian (EAS) AF: 0.287 AC: 1484 AN: 5164

South Asian (SAS) AF: 0.224 AC: 1080 AN: 4830

European-Finnish (FIN) AF: 0.0560 AC: 593 AN: 10596

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10199 AN: 67986

Other (OTH) AF: 0.152 AC: 321 AN: 2114

Alfa AF: 0.156 Hom.: 4059

Bravo AF: 0.137

Asia WGS AF: 0.235 AC: 820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.98
DANN	Benign	0.33
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4979219; hg19: chr9-110424020;