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_007058087.1(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_007058087.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374534	XR_007058087.1	n.-231G>A		upstream_gene_variant
LOC105374534	XR_925488.2	n.-231G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;