XR_939634.2:n.301-5415G>A

Variant names:

• chr4-189386130-G-A
• rs1107680
• XR_939634.2:n.301-5415G>A

Variant summary

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

The XR_939634.2(LOC105377614):​n.301-5415G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,082 control chromosomes in the GnomAD database, including 6,217 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 0.27 (6217 hom., cov: 33)
• Consequence: LOC105377614 XR_939634.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 0 publications found

Genes affected

LOC105377614 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41140 AN: 151964 Hom.: 6213 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.271 AC: 41157 AN: 152082 Hom.: 6217 Cov.: 33 AF XY: 0.278 AC XY: 20702 AN XY: 74342

African (AFR) AF: 0.153 AC: 6360 AN: 41498

American (AMR) AF: 0.343 AC: 5233 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3464

East Asian (EAS) AF: 0.432 AC: 2228 AN: 5156

South Asian (SAS) AF: 0.380 AC: 1833 AN: 4818

European-Finnish (FIN) AF: 0.404 AC: 4260 AN: 10556

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19574 AN: 67998

Other (OTH) AF: 0.257 AC: 543 AN: 2116

Alfa AF: 0.271 Hom.: 7063

Bravo AF: 0.259

Asia WGS AF: 0.407 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.76
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs1107680; hg19: chr4-190307284;