XR_939634.2:n.301-5436C>G

Variant names:

• chr4-189386109-C-G
• rs1869946
• XR_939634.2:n.301-5436C>G

Variant summary

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

The XR_939634.2(LOC105377614):​n.301-5436C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,064 control chromosomes in the GnomAD database, including 6,259 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 (6259 hom., cov: 33)
• Consequence: LOC105377614 XR_939634.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 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: 0.273 AC: 41446 AN: 151946 Hom.: 6253 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.403

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: 0.273 AC: 41471 AN: 152064 Hom.: 6259 Cov.: 33 AF XY: 0.280 AC XY: 20841 AN XY: 74306

African (AFR) AF: 0.161 AC: 6659 AN: 41488

American (AMR) AF: 0.343 AC: 5244 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3468

East Asian (EAS) AF: 0.433 AC: 2231 AN: 5152

South Asian (SAS) AF: 0.381 AC: 1835 AN: 4820

European-Finnish (FIN) AF: 0.403 AC: 4259 AN: 10566

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

European-Non Finnish (NFE) AF: 0.288 AC: 19574 AN: 67966

Other (OTH) AF: 0.257 AC: 543 AN: 2112

Alfa AF: 0.271 Hom.: 733

Bravo AF: 0.262

Asia WGS AF: 0.410 AC: 1426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.59
DANN	Benign	0.47
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs1869946; hg19: chr4-190307263;