rs1145625

Variant names:

• chr5-158225073-A-G
• rs1145625

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.158 in 151,964 control chromosomes in the GnomAD database, including 1,976 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 0.16 (1976 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23974 AN: 151844 Hom.: 1971 Cov.: 31

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.158 AC: 23997 AN: 151964 Hom.: 1976 Cov.: 31 AF XY: 0.162 AC XY: 12006 AN XY: 74266

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.164

Alfa AF: 0.145 Hom.: 3269

Bravo AF: 0.151

Asia WGS AF: 0.288 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1145625; hg19: chr5-157652081;