rs1025260

Variant names:

• chr5-153955577-A-T
• rs1025260
• XR_001742937.1:n.124-1109T>A

Variant summary

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

The XR_001742937.1(LOC107986464):​n.124-1109T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,086 control chromosomes in the GnomAD database, including 4,276 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 0.23 (4276 hom., cov: 32)
• Consequence: LOC107986464 XR_001742937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 3 publications found

Genes affected

LOC107986464 (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 (AFR) allele frequency at 95% confidence interval = 0.316 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: 0.226 AC: 34296 AN: 151968 Hom.: 4267 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.226 AC: 34328 AN: 152086 Hom.: 4276 Cov.: 32 AF XY: 0.225 AC XY: 16707 AN XY: 74338

African (AFR) AF: 0.320 AC: 13292 AN: 41476

American (AMR) AF: 0.180 AC: 2754 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3468

East Asian (EAS) AF: 0.109 AC: 562 AN: 5172

South Asian (SAS) AF: 0.114 AC: 551 AN: 4818

European-Finnish (FIN) AF: 0.268 AC: 2832 AN: 10558

Middle Eastern (MID) AF: 0.269 AC: 78 AN: 290

European-Non Finnish (NFE) AF: 0.187 AC: 12742 AN: 67988

Other (OTH) AF: 0.221 AC: 467 AN: 2112

Alfa AF: 0.210 Hom.: 431

Bravo AF: 0.227

Asia WGS AF: 0.138 AC: 478 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	1.5
DANN	Benign	0.77
PhyloP100		-0.057

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1025260;

hg19: chr5-153335137;