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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986464	XR_001742937.1	n.124-1109T>A		intron_variant	Intron 1 of 2

Ensembl

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

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 v4.3

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

Other links and lift over

dbSNP: rs1025260; hg19: chr5-153335137;