rs4129434

Variant names:

• chr1-208941027-C-T
• rs4129434
• XR_001738441.2:n.496-118857G>A

Variant summary

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

The XR_001738441.2(LOC107985255):​n.496-118857G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,090 control chromosomes in the GnomAD database, including 8,504 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 0.32 (8504 hom., cov: 32)
• Consequence: LOC107985255 XR_001738441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74
• Publications: 3 publications found

Genes affected

LOC107985255 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 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: 0.325 AC: 49390 AN: 151972 Hom.: 8506 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.325 AC: 49399 AN: 152090 Hom.: 8504 Cov.: 32 AF XY: 0.321 AC XY: 23841 AN XY: 74322

African (AFR) AF: 0.236 AC: 9790 AN: 41496

American (AMR) AF: 0.290 AC: 4430 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1563 AN: 3468

East Asian (EAS) AF: 0.228 AC: 1176 AN: 5156

South Asian (SAS) AF: 0.282 AC: 1361 AN: 4824

European-Finnish (FIN) AF: 0.341 AC: 3603 AN: 10560

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26240 AN: 67974

Other (OTH) AF: 0.347 AC: 733 AN: 2114

Alfa AF: 0.363 Hom.: 21277

Bravo AF: 0.317

Asia WGS AF: 0.246 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.011
DANN	Benign	0.37
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs4129434; hg19: chr1-209114372;