rs12519145

Variant names:

• chr5-177128522-G-A
• rs12519145

Your query was ambiguous. Multiple possible variants found:

• chr5-177128522-G-A
• chr5-177128522-G-C

Variant summary

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

The variant allele was found at a frequency of 0.199 in 152,080 control chromosomes in the GnomAD database, including 3,679 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 0.20 (3679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 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: 0.199 AC: 30313 AN: 151962 Hom.: 3669 Cov.: 32

Gnomad AFR AF: 0.0940

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.199 AC: 30338 AN: 152080 Hom.: 3679 Cov.: 32 AF XY: 0.206 AC XY: 15316 AN XY: 74344

African (AFR) AF: 0.0939 AC: 3896 AN: 41510

American (AMR) AF: 0.291 AC: 4434 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3472

East Asian (EAS) AF: 0.443 AC: 2291 AN: 5170

South Asian (SAS) AF: 0.331 AC: 1596 AN: 4824

European-Finnish (FIN) AF: 0.212 AC: 2234 AN: 10560

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14574 AN: 67966

Other (OTH) AF: 0.189 AC: 399 AN: 2110

Alfa AF: 0.186 Hom.: 1275

Bravo AF: 0.202

Asia WGS AF: 0.338 AC: 1179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.4
DANN	Benign	0.47
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs12519145; hg19: chr5-176555523;