chr4-23475859-G-A

Variant names:

• chr4-23475859-G-A
• rs12498626
• XR_007058437.1:n.3134-28148G>A

Variant summary

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

The XR_007058437.1(LOC105374524):​n.3134-28148G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,056 control chromosomes in the GnomAD database, including 3,347 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 0.20 (3347 hom., cov: 33)
• Consequence: LOC105374524 XR_007058437.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 2 publications found

Genes affected

LOC105374524 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 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: 0.198 AC: 30131 AN: 151938 Hom.: 3335 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.198 AC: 30174 AN: 152056 Hom.: 3347 Cov.: 33 AF XY: 0.201 AC XY: 14954 AN XY: 74314

African (AFR) AF: 0.281 AC: 11659 AN: 41464

American (AMR) AF: 0.231 AC: 3519 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3472

East Asian (EAS) AF: 0.284 AC: 1467 AN: 5160

South Asian (SAS) AF: 0.265 AC: 1279 AN: 4820

European-Finnish (FIN) AF: 0.157 AC: 1660 AN: 10570

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

European-Non Finnish (NFE) AF: 0.139 AC: 9441 AN: 67998

Other (OTH) AF: 0.185 AC: 390 AN: 2106

Alfa AF: 0.159 Hom.: 9337

Bravo AF: 0.208

Asia WGS AF: 0.273 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.88
DANN	Benign	0.44
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs12498626; hg19: chr4-23477482;