4-25113042-C-T

Variant names:

• chr4-25113042-C-T
• rs10939038
• XR_007058087.1:n.-231G>A

Variant summary

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

The XR_925488.2(LOC105374534):​n.-231G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,038 control chromosomes in the GnomAD database, including 9,948 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 0.34 (9948 hom., cov: 32)
• Consequence: LOC105374534 XR_925488.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• Publications: 3 publications found

Genes affected

LOC105374534 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 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: 0.336 AC: 50991 AN: 151920 Hom.: 9953 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.335 AC: 50987 AN: 152038 Hom.: 9948 Cov.: 32 AF XY: 0.332 AC XY: 24689 AN XY: 74318

African (AFR) AF: 0.145 AC: 6025 AN: 41446

American (AMR) AF: 0.363 AC: 5543 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1130 AN: 3470

East Asian (EAS) AF: 0.164 AC: 850 AN: 5174

South Asian (SAS) AF: 0.269 AC: 1297 AN: 4830

European-Finnish (FIN) AF: 0.435 AC: 4586 AN: 10536

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30256 AN: 67984

Other (OTH) AF: 0.353 AC: 746 AN: 2114

Alfa AF: 0.406 Hom.: 17259

Bravo AF: 0.324

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.83
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10939038; hg19: chr4-25114664;