rs12186500

Variant names:

• chr5-180749005-A-G
• rs12186500

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 0.414 in 152,096 control chromosomes in the GnomAD database, including 15,554 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 0.41 (15554 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.552 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: 0.415 AC: 63011 AN: 151978 Hom.: 15551 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.414 AC: 63014 AN: 152096 Hom.: 15554 Cov.: 32 AF XY: 0.414 AC XY: 30819 AN XY: 74370

African (AFR) AF: 0.154 AC: 6408 AN: 41544

American (AMR) AF: 0.434 AC: 6622 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1795 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1267 AN: 5178

South Asian (SAS) AF: 0.323 AC: 1555 AN: 4820

European-Finnish (FIN) AF: 0.582 AC: 6159 AN: 10580

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37804 AN: 67922

Other (OTH) AF: 0.421 AC: 889 AN: 2110

Alfa AF: 0.498 Hom.: 37926

Bravo AF: 0.395

Asia WGS AF: 0.270 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.9
DANN	Benign	0.74
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12186500; hg19: chr5-180176005; COSMIC: COSV53484911;